<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36512?offset=50 https://bioinformaticsonline.com/bookmarks/view/36476/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Fri, 04 May 2018 19:16:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36476/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structural accuracy of the resulting sequence. The package also includes a polisher module, which produces the final assembly of high nucleotide-level quality.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads Wed, 22 Aug 2018 10:40:27 -0500 https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads <![CDATA[SimLoRD: A read simulator for third generation sequencing reads]]> SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

  • The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
  • The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
  • Quality values and number of passes depend on fragment length.
  • Provided subread error probabilities are modified according to number of passes
  • Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

]]> Aaryan Lokwani https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads Fri, 31 Jan 2020 05:50:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads <![CDATA[HASLR: a tool for rapid genome assembly of long sequencing reads]]> HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. 

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads Mon, 04 May 2020 02:04:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads <![CDATA[HASLR: a hybrid assembler which uses both second and third generation sequencing reads]]> HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> BioStar https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly Tue, 17 Aug 2021 13:17:09 -0500 https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly <![CDATA[Bioinformatics tools for telomere to telomere assembly !]]> ● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)
● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)
● SQANTI3 – an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Rocío Amorín de Hegedüs @rocioadh)
● tama (Transcriptome Annotation by Modular Algorithms) – software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo @GenomeRIK)
● pbaa (PacBio Amplicon Analysis) – separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg @zevkronenberg)
● bellerophon – analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng @Yuanyuan929)
● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)
● JumboDB – tool for de Bruijn graph construction (Anton Bankevich @AntonBankevich)
● uLTRA – tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @krsahlin)
● LeafGo – workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini @ermini_luca)

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

 

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/27323/cutadapt Fri, 13 May 2016 04:54:50 -0500 https://bioinformaticsonline.com/bookmarks/view/27323/cutadapt <![CDATA[cutadapt]]> Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads.

Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Also, paired-end reads and even colorspace data is supported. If you want, you can also just demultiplex your input data, without removing adapter sequences at all.

Cutadapt comes with an extensive suite of automated tests and is available under the terms of the MIT license.

If you use cutadapt, please cite DOI:10.14806/ej.17.1.200 .

Address of the bookmark: https://cutadapt.readthedocs.io/en/stable/installation.html#quickstart

]]> Radha Agarkar https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data Fri, 04 Oct 2024 02:45:06 -0500 https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data <![CDATA[Libraries or management tools for high throughput sequencing data]]>
  • GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
    These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
  • LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

    • Variant calling and/or genotyping

    • DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
    • MindTheGap: Detection and assembly of large insertion variants
    • TakeABreak: reference-free inversion discovery tool
    • SVJedi: Structural Variant genotyper with long read data
    • SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

    Sequence assembly

    • MinYS: reference-guided genome assembly in metagenomics data
    • MTG-link: local assembly tool for linked-read data
    • Minia: De novo short read assembler
    • de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
    • Mapsembler2: Targeted assembly (not maintained)

    Managing k-mers & indexation

    • findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
      • fimpera extends findere adding the abundance information.
    • kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
    • kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
    • back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
    • Backpack Quotient Filter: k-mer indexing data structure with abundance
    • short read connector: Detect similar reads from potentially large read set
    • DSK: Count K-mer in sequences

    Pangenome graph manipulation

    • Pancat: Pangenome Comparison and Analysis Toolkit
    • GFAGraphs: a Python library to handle pangenome graph files in GFA format.

    Comparative metagenomics with k-mers

    Species and bacterial strains identification

    • ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
    • StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

    General-purpose sequencing data manipulation

    • GASSST: long read mapper
    • Leon: short read compressor (now included in GATB-core)
    • Bloocoo: short read corrector
    • BCALM: Construct compacted de Bruijn graphs (unitigs)

     Protein Structure

    • A_Purva: Contact Map Overlap solver
    • MD-Jeep: Distance Geometry solver
    • CSA: Comparative Structural Alignment

    Workflow

    • SLICEE: parallel execution of bioinformatics workflows

    Comparative Genomics

    • CASSIS: detection of rearrangement breakpoints
    • PLAST: intensive bank-to-bank sequence comparison
    • DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments
    ]]>     LEGE     https://bioinformaticsonline.com/bookmarks/view/30557/speedseq Fri, 20 Jan 2017 06:05:43 -0600 https://bioinformaticsonline.com/bookmarks/view/30557/speedseq <![CDATA[SpeedSeq]]> A flexible framework for rapid genome analysis and interpretation

    C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.

    http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html

    Address of the bookmark: https://github.com/hall-lab/speedseq

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/33840/awesome-perl-frameworks-libraries-and-software-part-3 Fri, 07 Jul 2017 04:10:32 -0500 https://bioinformaticsonline.com/pages/view/33840/awesome-perl-frameworks-libraries-and-software-part-3 <![CDATA[Awesome perl frameworks, libraries and software - PART 3]]>
  • fujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL.
  • formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms
  • fastly/fastly-perl - Fastly perl client
  • ewilded/SCARY - PHP Source Code Analyzer written in Perl (taint checking)
  • esobchenko/rest-google - REST::Google provides OO access to Google REST API from Perl
  • Ensembl/Bio-DB-HTS - Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
  • eblah/E-Blah-Forum - E-Blah is a Perl-based forum system started in 2001.
  • dominikschulz/Zabbix-Sender - A pure-perl implementation of zabbix-sender.
  • derf/Travel-Status-DE-IRIS - IRIS Perl API (German and partially european railway departure monitor)
  • Debian/devscripts - Mirror of https://anonscm.debian.org/cgit/collab-maint/devscripts.git
  • ddmitov/camel-doctor - Desktop HTML User Interface for the default Perl 5 Debugger :dromedary_camel:
  • dan-blanchard/io-storm - :zap: Perl support for Apache Storm distributed computation system.
  • dajobe/logger - Perl IRC logger
  • dagolden/Hash-Ordered - A compact, pure-Perl ordered hash class
  • dagolden/getopt-lucid - (Perl) Clear, readable syntax for command line processing
  • craigslist/perl-AnyEvent-Redis-Federated - An event-based redis client that implements client-side sharding in Perl.
  • cosimo/perl5-device-modem - Device::Modem CPAN module, interface to any AT-command-set based device
  • CindyLinz/Perl-AnyEvent-MySQL - Pure Perl AnyEvent socket implementation of MySQL client
  • chorny/test-warn - Perl extension to test methods for warnings
  • cho45/List-Enumerator - List::Enumerator is like ruby's Enumerator. (Perl)
  • bingos/module-install-readmefrompod - (perl) A Module::Install extension to automatically convert POD to a README
  • bingos/bot-gumbynet - (perl) The GumbyNET bot code
  • aufflick/p5-net-apns-persistent - Persistent Apple APNS interface for Perl 5
  • ddmitov/perl-executing-browser - HTML User Interface for Perl 5 Desktop Applications :dromedary_camel:
  • phatblat/app-store-rank - A simple Perl script which scrapes the 62 app stores worldwide for the current app ranking
  • Easy-Forex/Verify-emails - Quick perl script to check a list of email addresses for valid and bogus.
  • warewolf/Procmon - A perl command toolkit for analysis of XML procmon logs
  • typester/data-amf - perl module for serialize/deserialize adobe's AMF data
  • thibaultduponchelle/tryperl - Try Perl: learn the basics of the Perl language in your browser
  • syohex/new-tohoho - Modernize 「とほほの perl入門」
  • simcop2387/perlbuut - new version of perlbot, based on buubot
  • rjray/image-size - A Perl module to read the dimensions of images in several popular formats
  • perigrin/flexo-bot - A Rewrite of the Bender IRC bot from irc.perl.org using the Adam/Moses framework
  • norm/p5-Media - Perl modules and scripts for handling the conversion and storage of media
  • nkakuev/list-cpp-warning-options - A simple Perl script that prints GCC warning options you can apply to C++ code.
  • mscoutermarsh/RRD-to-CSV - Perl script to convert RRD data to CSV
  • mones/clawsker - This is a clone from main repository at http://git.claws-mail.org: Clawsker is a Perl-GTK2 applet to edit hidden preferences for Claws Mail, and to do it in a safe and user friendly way, preventing users from raw editing of configuration files.
  • mackers/passook - Passook is a perl script that automatically generates passwords. Passook is customizable so that you can choose different levels between a very pronounceable or a very secure password. Passook can be run in a unix shell or as a cgi script.
  • lecstor/PDF--Boxer - Perl module to create PDF documents from "simple" templates.
  • jmcnamara/app-pod2epub - A Perl Module for converting Pod to ePub eBooks.
  • jjn1056/Example-PlackStreamingAndNonblocking - Examples of Perl Plack / PSGI streaming and nonblocking
  • hoytech/Valence-p5 - Perl interface to valence/electron GUI toolkit
  • erinspice/geni-automerge - A tool written in Perl using the Geni.com API which automatically merges sufficiently similar profiles.
  • eilara/camel-defense - A very simple tower defense game in Perl
  • clintongormley/ElasticSearchX-Autocomplete - ElasticSearchX::Autocomplete is a Perl module which gives you frequency (and optionally geolocation)-sensitive autocomplete suggestions based on your data
  • audreyt/encode-hanconvert - [Perl] Modules and scripts for Traditional and Simplified Chinese mappings
  • szabgab/perltv.org - The source code of the Perl TV
  • rhandom/perl-net-server - Perl Module Net::Server
  • plotly/Perl-API - Perl-API for beautiful, interactive, & shareable graphs
  • MerijntjeTak/vyattaLookingGlass - Looking glass for the Vyatta routing suite
  • KES777/Devel-DebugHooks - Perl debugger
  • jonasbn/perl-workflow - Simple, flexible system to implement workflows
  • inway/mojo-rabbitmq-client - Mojo::IOLoop based RabbitMQ (AMQP) client
  • ingydotnet/yaml-pm - YAML Perl Module
  • gtsafas/mailgun.perl - Perl wrapper for mailgun
  • abaez/perl - Learning Perl
  • technix/Perl-Analyzer - Perl source analyzer - view namespaces, dependencies, inheritance and much more
  • zigorou/perl-json-patch - A Perl implementation of JSON Patch
  • Yaribz/SPADS - SpringRTS Perl Autohost for Dedicated Server
  • vti/app-prf - Perl refactoring tool
  • TvdW/perl-DBD-Cassandra - DBD::Cassandra is a DBI driver for Cassandra/CQL3
  • topaz/perl-mandelbrot - Interactive Mandelbrot set renderer/explorer for your terminal.
  • tociyuki/libtext-ampita-perl - Template generator from a xhtml document and runtime for it.
  • tene/perl6-sqlite - SQLite3 for Perl 6
  • smarx/waz-storage-perl - Small library for working with Windows Azure storage from Perl
  • scottchiefbaker/perl-git-prompt - Git extension for the bash prompt
  • sbober/levitation-perl - perl port of scy's levitation
  • salva/p5-Net-SFTP-Foreign - Perl SFTP client
  • russoz/perltests - Small scripts to test constructs - mostly for myself.
  • robrwo/Perl-Rewrite - Munge Perl Code
  • rjbs/IPC-Run3 - (Perl) run a subprocess with input/ouput redirection
  • rjbs/Email-Simple - the Email-Simple perl distribution
  • ritou/p5-oidc-lite - OIDC::Lite - Perl Library of OpenID Connect
  • pjf/WebService-HabitRPG - Access the HabitRPG API from Perl
  • pjf/trillr - Perl tip example code
  • PerlBone/PerlBone - PerlBone allows you to write Arduino Style software in Perl for the BeagleBone. It is to Perl what BoneScript is to Javascript
  • Ovid/code-cutnpaste - Find cut-n-pasted Perl code
  • mfontani/Net-Amazon-Route53 - Perl interface to Amazon's Route 53 service
  • maxmind/GeoIP2-perl - Perl API for MaxMind's GeoIP2 web services and databases
  • maros/CatalystX-I18N - Perl I18N Toolkit for the Catalyst MVC
  • marcusramberg/text-simpletable - The Text::SimpleTable perl distribution
  • lovelle/perl-disque - Perl client for Disque, an in-memory, distributed job queue
  • leto/math--matrixreal - Matrices of real numbers in Perl
  • Klortho/Physics-Unit - Perl Physics::Unit module
  • kentaro/perl-project-libs - Include modules libs automatically
  • karpet/search-query-perl - Search::Query - polyglot query parsing
  • jplindstrom/p5-Devel-PerlySense - CPAN module Devel::PerlySense
  • hvoers/PNL - Site for Perl mongers in NL
  • HouzuoGuo/PerlDB - This is a programming exercise, do not use in serious code.
  • hirose31/p5-InfluxDB - Perl client library for InfluxDB
  • grantm/XML-SAX - Simple API for XML including pure Perl parser
  • GeneticGenesis/Perl-Ferment - Yet another tool to manage perl installs in your home directory.
  • Ensembl/ensembl-funcgen - Ensembl Funcgen Perl API and SQL schema
  • dk/Win32-GuiTest - Perl GUI Test Utilities
  • depesz/Pg--Explain - Pg::Explain Perl module
  • dann/p5-perl-metrics-lite - Pluggable Perl Metrics System
  • daisieh/phylogenomics - (Mostly) Perl scripts that do something related to phylogenomic analysis.
  • carwynmoore/perl-nats - A Perl client for the NATS messaging system
  • briandfoy/test-prereq - (Perl) check if Makefile.PL has the right pre-requisites
  • briandfoy/cpan-packagedetails - (Perl) This is what the module does
  • bingos/cpanplus-yacsmoke - (perl) Yet Another CPANPLUS Smoke Tester
  • beanz/net-mqtt-perl - Perl implementation of MQTT Protocol (http://mqtt.org)
  • perl6/book - Using Perl 6 - an unfinished book about Perl 6
  • lukec/stripe-perl - Perl library to connect to the Stripe API
  • c0bra/image-wordcloud-perl - Perl module for generating pretty wordcloud images
  • bradfitz/set-consistenthash-perl - consistent hashing library for Perl
  • wolfman2000/Perl-6-Pastebin - A pastebin written in Perl 5 to host content specifically meant for Perl 6.
  • njh/perl-net-rtp - Perl Module : Send and receive RTP packets (RFC3550)
  • beanz/net-pachube-perl - Perl Interface to Pachube
  • apparentlymart/perl-anyevent-websocket - WebSocket implementation for AnyEvent
  • tsee/ZMQ-Declare-Perl - The ZMQ::Declare Perl module for declarative use of 0MQ
  • sjohnston/Net-Zabbix - Perl wrapper for Zabbix API
  • reneeb/Perl-Critic-OTRS - A collection of Perl::Critic policies to program in the OTRS way.
  • masak/csv - A parser for CSV (comma-separated values) files for Perl 6
  • jtbraun/Parse-RecDescent - Perl module for generating recursive-descent parsers
  • jjn1056/perl-recruiting-web - webpages for helping recruiters and perl programmers understand each other better
  • chef-boneyard/chef-install - A perl based installer for Chef
  • pvande/Template-Mustache - Drawing Mustaches on Perl, for fun and profit
  • schwern/Paths - Grand Unified Perl File and Directory Objects
  • schwern/Gravatar-URL - Perl module to make URLs for Gravatars from an email address
  • p5-shorten/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
  • juliensobrier/Net-Google-SafeBrowsing2 - Google Safe Browsing v2 library for Perl
  • EntropyOrg/p5-Devel-IPerl - :microscope::books: Perl language kernel for Jupyter http://jupyter.org/
  • PerlChina/HeadFirstMoose - 使用Perl + Moose实现《Head First Design Pattern》的大部分例子
  • mudler/GitInsight - Predict your github contributions using Bayesian inference and Markov chain with perl and PDL
  • dagolden/File-chdir - (Perl) a more sensible way to change directories
  • potyl/perl-App-deckjs2pdf - Convert a Deck.JS presentation to PDF
  • Perl-Toolchain-Gang/Sub-Uplevel - (Perl) apparently run a function in a higher stack frame
  • mlawren/p5-OptArgs - Integrated option and argument processing for Perl scripts
  • masterzen/redis-snmp - A perl net-snmp agentX to export Redis performance counters
  • masochist/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
  • jeffa/DesignPatterns-Perl - Perl (with Moose) implementations of the Gang of Four Design Patterns
  • agentzh/makefile-parser-pm - Perl CPAN module Makefile::Parser - A simple parser for Makefiles
  • Real-Gecko/filemin - File manager for Webmin written completely in perl
  • andreas-marschke/nagios-nrpe - A pure perl implementation of the Nagios NRPE daemon and client
  • syohex/zsh-perl-completions - zsh completions for Perl utilties
  • pclinger/SonyCameraRemote - Sony Camera Remote API - Perl Implementation
  • patch/cldr-number-pm5 - CLDR::Number (Perl 5): Localized number formatters using the Unicode CLDR
  • ollyg/Net-CLI-Interact - Development of Net::CLI::Interact Perl distribution
  • nothingmuch/continuation-delimited - delimited continuations for Perl 5
  • nmelnick/whatbot - whatbot: A sane bot for most chat applications, written in modern Perl
  • naoya/list-rubylike - Ruby-like list operations for perl
  • miyagawa/CPAN-Any - Install Perl modules using any CPAN clients
  • miki/Algorithm-LSH - perl implementation of Locality Sensitive Hashing
  • kimmel/basic-perl-template-for-cli - A basic template for Perl applications that take and parse command line options. Based on the ideas from Perl Best Practices and the GNU style long options reference. It uses only Standard Modules to maintain portability.
  • gardejo/moose-presentations - Perl Moose course in Japanese
  • dpavlin/Biblio-RFID - perl tools to use different RFID readers for library use
  • chef/chef-install - A perl based installer for Chef
  • bingos/smokebrew - (perl) Automated Perl building and installation for CPAN Testers
  • andrewrjones/perl5-App-MP4Meta - Apply iTunes-like meta data to an mp4 file
  • admc/irssi-growlnotify - Creating Growl notifications from various Irssi events, using growlnotify and Irssi Perl.
  • plack/psgi-specs - PSGI (Perl WSGI) specifications
  • libwww-perl/uri - The Perl URI:: module
  • autarch/DateTime.pm - A date and time object for Perl
  • zostay/P6SGI - Proposed Standard for Perl 6 Web Server Gateway Interface Specification
  • cooper/yiria - the current generation of juno-ircd, an IRC server daemon written in the Perl programming language. it's very modular and event-driven, designed specifically to be extensible and aims to implement all modern features of IRC, including those of many recently-defined specifications.
  • wertarbyte/hetzner-rdns - update reverse DNS settings for systems hosted at Hetzner; a successor (hetzner-robot-perl) is in preparation to utilise the webservice interface
  • spencertipping/canard - A functional concatenative language implemented in Linux/AMD64 machine code and self-modifying perl
  • sni/Monitoring-Generator-TestConfig - Perl extension for generating test monitoring configurations (nagios/icinga/shinken)
  • slazar/Panasonic-LF20-control - Perl Scripts to control the Panasonic LF20 LCD TV Series
  • sabujp/nfsSpeedTest - nfsSpeedTest is a wrapper for dd written in Perl. It was created mainly for testing the performance of file systems or network file shares (e.g. NFS), but can be used for generating large files (e.g. swap files) or for testing the network
  • quietfanatic/link-c - Easily use C libraries in Rakudo Perl 6
  • pjain/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
  • nightsailer/net-sinaweibo - A lightweight Perl OAuth api for SinaWeibo(新浪微博)
  • mbethke/Ashafix - A Postfixadmin clone in Perl/Mojolicious
  • kzys/test-mock-recorder - Record-and-verify style mocking library for Perl
  • kpumuk/mysqlsla-bdb - MySQL Slow Logs Analyzer optimized to work with huge logs (use BerkeleyDB instead of perl hashes)
  • hernan604/Web-IRC - The purpose of Web::IRC is to help team communication. Web::IRC uses channel concept from IRC. Slack.com clone in perl <3
  • duckduckgo/p5-duckpan-installer - DuckPAN Perl Installer
  • dnmfarrell/Perly-Bot - a RSS trawler and social media broadcaster
  • PDLPorters/PDL-Stats - Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.
  • CPAN-API/metacpan-client - Home of the official MetaCPAN Perl API client.
  • rrb3942/perl-Asterisk-AMI - A Perl module for interfacing with the Asterisk Management Interface.
  • rafl/perlfaq - History of the perlfaq distribution before it got moved to https://github.com/tpf/perlfaq
  • mithun/perl-tmdb - TMDB - Perl wrapper for The MovieDB API
  • hyphaltip/htbda_perl_class - High Throughput Biological Data Analysis using Perl
  • gmcharlt/marc-perl - MARC/Perl (mirror of git://git.code.sf.net/p/marcpm/code)
  • cosimo/perl5-http-dav - Perl5 HTTP::DAV CPAN module, interface to WebDAV-enabled HTTP servers
  • copperly/Perl-Tutorial - Tutorial for Perl
  • apocalypse/perl-dist-zilla-plugin-authority - add an $AUTHORITY to your packages
  • DrHyde/perlscripts - Random scripts
  • perl6/DBIish - Database interface for Perl 6
  • shlomif/mastering-perl - A copy of brian d foy's mastering-perl book.
  • Prajithp/letsencrypt-cpanel - cPanel/WHM plugin for Let's Encrypt client (uses perl and WHM API)
  • mikecardwell/pipe2imap - Pipe2IMAP is a Perl script that will take IMAP options from the command line arguments, and an email from a PIPE, and will deliver the message via IMAP
  • silverstripe-labs/silverstripe-unidecode - Unidecode is a PHP version of the perl module Text::Unicode. It takes UTF-8 data and tries to represent it in US-ASCII characters.
  • exhuma/jsttyplay - A set of scripts written in Perl and JavaScript to allow ttyrec logs to be played back in a web browser.
  • demianriccardi/HackaMol - Object-Oriented Perl 5, Moose Library for Molecular Hacking
  • davorg/www-shorten - Perl interface to various URL-shortening sites
  • agentzh/queue-memcached-buffered - Perl client library for memcacheq operations
  • toronto-perl-mongers/tpm-website - Toronto Perl Mongers Website
  • odyniec/p5-WebService-Amazon-Route53 - Perl interface to Amazon Route 53 API
  • neilb/perl-hub - Proof of concept for "front page for the perl community"
  • mschilli/proc-simple-perl - Proc::Simple CPAN Module
  • makamaka/geohex-perl - geohex perl implementation (Geo::Hex)
  • gslin/thrift-perl - Perl module of Thrift
  • djzort/Net-DHCP - Perl module Net::DHCP
  • cosimo/perl5-test-device-serialport - A mock object to test virtual serial port-based devices
  • afair/resque-perl - Resque ported to perl
  • PerlChina/Newbie-Gift - A tool suite for perl newbie.
  • Perl-Email-Project/Email-Send - perl library for sending email
  • Lemonade-Stand/Lemonade - Perl E-commerce Solution
  • atomicules/TTYtter - Unofficial maintenance and mirror of Floodgap's TTYtter: an interactive console text-based command-line Twitter client and Perl platform (whew!)
  • worldmind/perl-test-code-quality-template - Some tests for non-functional testing - you can copy these test to any your perl project
  • dpavlin/perl-fuse - write filesystems in Perl using FUSE
  • rjbs/Email-Valid - perl library to validate email addresses
  • masak/gge - Glacial Grammar Engine -- a Perl 6 grammar engine written in Perl 6
  • masak/druid - A connection-oriented board game written in Perl 6
  • harisekhon/lib - Perl & Python Utility Library for my other repos
  • tempire/riak-tiny - Perl interface to Riak without Moose
  • oz/tiny_wiki - 50 lines of Perl to play around with Dancer and KiokuDB
  • goozbach/perl-Net-Disqus - A Perl library for the Disqus API -- Deprecated
  • borisdaeppen/VM-JiffyBox - Perl API for JiffyBox
  • apeiron/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
  • ajolma/geoinformatica - Geoinformatica is a geospatial toolkit that builds on GDAL, Perl and GTK+
  • Weborama/Riak-Light - Fast and lightweight Perl client for Riak
  • zostay/owasp-esapi-perl - OWASP Enterprise Security API for Perl
  • yannk/perl-net-appnotifications - perl5 interface to www.appnotifications.com: easily deliver push notifications to your iPhone
  • three18ti/Reddit.pm - Perl wrapper for the reddit API
  • sukria/Test-TinyMocker - Minimal yet very useful mocker for Perl
  • solgenomics/yapri - Yet Another Perl R Inteface.
  • rclasen/workout - Workout file perl library
  • pshangov/perldoc-vim - Perldoc viewer for vim with syntax highlighting
  • olof/transmission-client - Perl interface to Transmission bittorrent client
  • ogawa/cybozu2ical-perl - Converting Cybozu Office Scheduler data to iCalendar format.
  • motemen/perl5-Print-Indented - Outputs indented as per source code indentation
  • miknight/pisg - Perl IRC Statistics Generator
  • melo/bash-completion - A Perl distribution to create your own bash completion solutions
  • mantovani/SPPM-Web - São Paulo Perl Mongers website.
  • jzawodn/perl-Algorithm-TopPercent - A perl module for tracking the top-N most frequent items in a streaming data set using fixed memory.
  • jmlynesjr/wxPerl-Module-Examples - wxPerl-Module-Examples not from the wxBook
  • doy/parse-keyword - DEPRECATED: write syntax extensions in perl
  • chromatic/Test-MockObject - The Test::MockObject Perl 5 library from the CPAN
  • chrisa/perl-Net-ZooKeeper - Net::ZooKeeper Perl module
  • apparentlymart/activity-streams-perl - Activity Streams Library for Perl
  • andrewalker/p5-webservice-digitalocean - Perl module for DigitalOcean's RESTful API
  • Starlink/perl-Astro-FITS-HdrTrans - Perl module for performing astronomical metadata header translations from FITS to generic and back.
  • Rio-Perl-Mongers/rio.pm.org - Site da Rio Perl Mongers
  • sitaramc/gitolite - Hosting git repositories -- Gitolite allows you to setup git hosting on a central server, with very fine-grained access control and many (many!) more powerful features. [IMPORTANT: please click and read the WIKI link above before submitting issues, pull requests, etc] IMPORTANT: PLEASE READ Nov 2 2014 UPDATE ABOUT DONATIONS -- see wiki
  • openresty/lua-nginx-module - Embed the Power of Lua into NGINX
  • sarabander/sicp-pdf - SICP PDF with Texinfo and LaTeX source
  • openresty/ngx_openresty - Turning Nginx into a Full-fledged Web App Server
  • petdance/ack - This repository is for ack 1.x, which is no longer being maintained. DO NOT SUBMIT ISSUES HERE. ack 2.0 has a new GitHub project at
  • openresty/nginx-tutorials - Nginx Tutorials
  • creaktive/rainbarf - CPU/RAM/battery stats chart bar for tmux (and GNU screen)
  • thoughtbot/rcm - rc file (dotfile) management
  • prey/prey-bash-client - Bash client for the Prey anti-theft software (Mac, Windows, Linux). The original.
  • lulzlabs/AirChat - Free Communications For Everyone.
  • k4rthik/git-cal - github like contributions calendar on terminal
  • munin-monitoring/contrib - Contributed stuff for munin (plugins, tools, etc...)
  • duckduckgo/duckduckgo - DuckDuckGo Instant Answer Infrastructure
  • nbs-system/naxsi - NAXSI is an open-source, high performance, low rules maintenance WAF for NGINX
  • DHowett/theos - Unified cross-platform iPhone Makefile system
  • git-deploy/git-deploy - Tool to manage using git as a deployment management tool
  • munin-monitoring/munin - Main repository for munin master / node / plugins
  • theory/sqitch - Sane database change management
  • jonreid/XcodeCoverage - Code coverage for Xcode projects
  • dalibo/pgbadger - a fast PostgreSQL Log Analyzer
  • nferraz/st - simple statistics from the command line
  • yuki-kimoto/gitprep - Github clone. you can install Github system into your unix/linux machine.
  • miyagawa/cpanminus - cpanminus - get, unpack, build and install modules from CPAN
  • sullo/nikto - Nikto web server scanner
  • sontek/dotfiles - My configuration files (.screenrc, .vimrc, .weechat, .bashrc, .gitconfig, etc)
  • PenturaLabs/Linux_Exploit_Suggester - Linux Exploit Suggester; based on operating system release number
  • RexOps/Rex - A framework for server orchestration and to simplify system administration
  • hokaccha/nodebrew - Node.js version manager
  • pasky/speedread - A simple terminal-based open source Spritz-alike (per-word RSVP aligned on optimal reading points)
  • plack/Plack - PSGI toolkit and server adapters
  • get-iplayer/get_iplayer - A utility for downloading TV and radio from BBC iPlayer
  • jfhovinne/jFeed - jQuery RSS/ATOM feed parser plugin
  • openresty/lua-resty-redis - Lua redis client driver for the ngx_lua based on the cosocket API
  • StefanSchroeder/Golang-Regex-Tutorial - Golang - Regular Expression Tutorial
  • openresty/nginx-systemtap-toolkit - Real-time analyzing and diagnosing tools for Nginx based on SystemTap
  • webfrogs/xcode_shell - shell script that used to auto-build xcode project
  • linode/cli - Command-line interface to the Linode platform
  • agentzh/code2ebook - Generate ebooks in various formats from source trees in various programming languages
  • timkay/aws - Easy command line access to Amazon EC2, S3, SQS, ELB, and SDB (new!)
  • webmin/webmin - Webmin source code
  • freebsdgirl/ggautoblocker - Good Game Auto Blocker
  • openresty/headers-more-nginx-module - Set, add, and clear arbitrary output headers
  • swcarpentry/bc - This repository is now frozen - please see the note below.
  • sm/sm - S{cripting,ystem,tack} Management (SM) Framework (Core)
  • alestic/ec2-consistent-snapshot - Initiate consistent EBS snapshots in Amazon EC2
  • bestpractical/rt - Request Tracker, an enterprise-grade issue tracking system
  • trapd00r/ls-- - ls on steroids
  • movabletype/movabletype - Movable Type
  • gotgit/gotgit - Errata and resources for GotGit: a book about Git in Chinese
  • ljunkie/plexWatch - Notify and Log watched content on a Plex Media Server
  • joeyh/myrepos - Multiple Repository management tool
  • xypiie/spread0r - spread0r is a txt reader, which makes your reading twice as fast as usual
  • linode/longview - Linode Longview Agent
  • philovivero/distribution - Short, simple, direct scripts for creating ASCII graphical histograms in the terminal.
  • mysociety/fixmystreet - This is mySociety's popular map-based reporting platform: easy to install in new countries and regions
  • spencertipping/js-in-ten-minutes - JavaScript in Ten (arbitrarily long) Minutes
  • kazeburo/GrowthForecast - Lightning Fast Graphing/Visualization
  • qooob/authentic-theme - Webmin/Usermin/Virtualmin/Cloudmin theme based on Bootstrap and Font Awesome
  • jbittel/httpry - HTTP logging and information retrieval tool
  • zakk4223/CocoaSplit - Stream/record your desktop/webcam to twitch/owned etc.
  • miyagawa/github-growler - Growl github updates
  • VividCortex/johnny-deps - Barebones dependency manager for Go.
  • dotphiles/dotphiles - A community driven framework of dotfiles.
  • CPAN-API/metacpan-web - Web interface for MetaCPAN
  • worlduniting/bookshop - bookShop is a publishing framework for html-to-pdf/(e)book toolchain happiness and sustainable productivity.
  • duncs/clusterssh - Cluster SSH - Cluster Admin Via SSH
  • leedo/noembed - oEmbed gateway service with additional non-oEmbed sources
  • cxreg/smartcd - Alter your bash (or zsh) environment as you cd
  • perl-catalyst/catalyst-runtime - The Elegant MVC Web Application Framework
  • Flipkart/HostDB - HostDB: a new tool to help manage data center inventory and write applications around it.
  • metabrainz/musicbrainz-server - The official musicbrainz-server codebase
  • monsieurvideo/get-flash-videos - Download or play videos from various Flash-based video hosting sites, without having to use the Flash player.
  • c9s/Vimana - Vimana is an easy to use system for searching , installing, and downloading vim script. Vimana provides a command-line interface such like aptitude programe on Debian linux, for you to search , download , install , upgrade scripts from http://www.vim.org (vimonline site).
  • Logitech/slimserver - Server for Logitech Squeezebox players. This server is also called Logitech Media Server
  • weijianwen/SJTUThesis - XeLaTeX templates for Shanghai Jiao Tong University (SJTU) thesis
  • hadley/ggplot2-book - The ggplot2 book
  • irssi/scripts.irssi.org - Script Repository for Irssi
  • bucardo/check_postgres - Nagios check_postgres plugin for checking status of PostgreSQL databases
  • harisekhon/nagios-plugins - Advanced Nagios Plugins - Hadoop, NoSQL datastores. Extends Nagios monitoring capabilities significantly further in to the application layer including Hadoop, Big Data, NoSQL and Web Scale technologies, APIs etc.
  • benbernard/RecordStream - commandline tools for slicing and dicing JSON records.
  • iberianpig/xSwipe - Multitouch gestures on X11, Linux
  • jimeh/manservant - Browse man pages in style with your personal manservant.
  • joeyh/ikiwiki - a wiki compiler
  • Zentyal/zentyal - Linux Small Business Server
  • yaoweibin/nginx_ajp_module - support AJP protocol proxy with Nginx
  • CPAN-API/cpan-api - A free, open API for everything you want to know about CPAN
  • neldredge/mathgen - See http://thatsmathematics.com/mathgen/
  • jtaby/Waldo - A generic port of TextMate's Find-In-Project, with associated MacVim plugin
  • broquaint/Gitalist - A modern git web viewer
  • rtomayko/shocco - shocco is a quick-and-dirty, literate-programming-style documentation generator for / in POSIX shell
  • pjf/exobrain - Automate your life with Exobrain
  • miyagawa/plagger - Pluggable RSS/Atom aggregator
  • justone/dotfiles - Dotfiles
  • jsierles/chef_cookbooks_deprecated - Opinionated chef recipes for Ubuntu/Debian. Manage nginx, unicorn, UNIX user accounts, postgresql, and more!
  • mattiasgeniar/varnish-4.0-configuration-templates - Configuration templates used for Varnish 4.0 implementations.
  • openresty/lua-resty-mysql - Nonblocking Lua MySQL driver library for ngx_lua
  • proger/eflame - Flame Graph profiler for Erlang
  • openresty/stapxx - Simple macro language extentions to systemtap
  • dkogan/feedgnuplot - Tool to plot realtime and stored data from the commandline, using gnuplot. This is the repo for 'feedgnuplot' on CPAN
  • wbraswell/rperl - RPerl Compiler
  • petdance/bobby-tables - bobby-tables.com, the site for preventing SQL injections
  • pshved/timeout - A script to measure and limit CPU time and memory consumption of black-box processes in Linux
  • openresty/srcache-nginx-module - Transparent subrequest-based caching layout for arbitrary nginx locations.
  • dockerana/dockerana - Docker Monitoring with support for Grafana and Graphite
  • OTRS/otrs - The OTRS framework.
  • bucardo/bucardo - Bucardo multimaster and master/slave Postgres replication
  • rjbs/Dist-Zilla - scary tools for building CPAN distributions
  • kjellm/munin-mysql - Improved MySQL Graphs for Munin
  • holygeek/git-number - Use numbers for dealing with files in git
  • s-aska/dropbox-api-command - Dropbox API wrapper command.
  • pintsized/ledge - A Lua application for OpenResty, providing scriptable HTTP cache functionality for Nginx.
  • rcarmo/textwrangler-bbedit-solarized - solarized color scheme for BBEdit and TextWrangler
  • lamw/vghetto-scripts - Various virtuallyGhetto scripts for VMware based solutions
  • tokuhirom/Amon - yet another web application framework
  • cschneid/irclogger - Sinatra based irclogger.com
  • andrewning/sortphotos - SortPhotos is a Python script that organizes photos and videos into folders using date/time information
  • pintsized/lua-resty-http - Lua HTTP client cosocket driver for OpenResty / ngx_lua.
  • jamesc/nagios-plugins-rabbitmq - A set of nagios checks for RabbitMQ using the management interface
  • kazeburo/cloudforecast - the server metrics gathering
  • zigdon/twirssi - An irssi script allowing the use of Twitter from within the IRC client.
  • ganglia/gmetric - Repository of user-contributed gmetric scripts
  • joemiller/collectd-graphite - collectd plugin for sending data to graphite
  • naoya/md2inao - Convert markdown to inao-format for WEB+DB PRESS
  • inverse-inc/packetfence - PacketFence is a fully supported, trusted, Free and Open Source network access control (NAC) solution. Boasting an impressive feature set including a captive-portal for registration and remediation, centralized wired and wireless management, powerful guest management options, 802.1X support, layer-2 isolation of problematic devices; PacketFence can be used to effectively secure networks small to very large heterogeneous networks.
  • devd/Academic-Writing-Check - check for passive words, weasel words, duplicate words, typographical errors and words strunk & white don't like
  • yoshinorim/mha4mysql-manager - Development tree of Master High Availability Manager and tools for MySQL (MHA), Manager part
  • yaoweibin/ngx_http_substitutions_filter_module - a filter module which can do both regular expression and fixed string substitutions for nginx
  • yaoweibin/nginx_syslog_patch - add the full syslog feature to Nginx
  • jjl/get_iplayer - A utility for grabbing tv and radio from BBC iPlayer. Phil Lewis has stopped developed it so I've forked it.
  • kost/dvcs-ripper - Rip web accessible (distributed) version control systems: SVN/GIT/HG...
  • mrash/fwknop - Single Packet Authorization > Port Knocking
  • majutsushi/urxvt-font-size - Change the urxvt font size on the fly
  • apenwarr/gitbuilder - Auto-builds and tests all the branches of your git projects, showing pass/fail results on a web page/RSS feed. Isolates failures to the first commit that caused the problem.
  • tangledhelix/dotfiles - My dotfiles
  • shabble/irssi-scripts - Repo to store some personal irssi scripts
  • kud/jpegrescan - JPEGrescan: losslessly shrink any JPEG file.
  • gregkh/bti - bash twitter ididocy
  • woothee/woothee - User-Agent parser/classifier for multi languages
  • spencertipping/nfu - Numeric Fu for the command line
  • davidbauer/Instacurate - Turn your Twitter timeline into a personalised news site, in an instant. Fetches links from your timeline and displays them in a discovery friendly design.
  • yuri-gushin/Roboo - Roboo - HTTP Robot Mitigator
  • kni/redis-sharding - Redis Sharding is a multiplexed proxy-server, designed to work with the database divided to several servers.
  • tempire/MojoExample - Mojolicious example with DBIx::Class schema load, deploy, fixtures, and tests.
  • reyjrar/es-utils - ElasticSearch Utilities
  • omniti-labs/omnipitr - Advanced WAL File Management Tools for PostgreSQL
  • GDSSecurity/PadBuster - Automated script for performing Padding Oracle attacks
  • openresty/rds-json-nginx-module - An nginx output filter that formats Resty DBD Streams generated by ngx_drizzle and others to JSON
  • zaf/asterisk-speech-recog - Speech recognition script for Asterisk that uses google's speech engine.
  • Ibmurai/Markdown.codaplugin - A Markdown plugin for Coda.
  • oetiker/SmokePing - The Active Monitoring System
  • openresty/lua-resty-upload - Streaming reader and parser for http file uploading based on ngx_lua cosocket
  • nriley/Pester - Simple, disposable alarms and timers for OS X.
  • dabockster/Smackbook-Yosemite - Updated Smackbook script for OS X Yosemite
  • cloudflare/lua-resty-logger-socket - Raw-socket-based Logger Library for Nginx (based on ngx_lua)
  • simpl/ngx_mongo - Non-blocking upstream module for Nginx to connect to MongoDB
  • iafan/Hacksby - Description and unofficial implementation of Furby's audio protocol
  • NixOS/hydra - Hydra, the Nix-based continuous build system
  • WolverineFan/YNABLinuxInstall - Install script for YNAB 4 on Linux
  • SPORE/specifications - SPORE specifications
  • xchataqua/xchataqua - An IRC client, OS X native front-end for XChat ( http://itunes.apple.com/app/id447521961 )
  • jfrazelle/dotfiles - My dotfiles
  • ytoolshed/pogo - Pogo is an agent-based system for running interruptive commands safely on thousands of machines in parallel
  • openresty/lua-resty-websocket - WebSocket support for the ngx_lua module (and OpenResty)
  • jzawodn/mytop - a "top" clone for MySQL
  • fonnesbeck/Bios8366 - Advanced Statistical Computing at Vanderbilt University's Department of Biostatistics
  • dbsrgits/dbix-class - Official github remote for git.shadowcat.co.uk DBIx-Class.git
  • bricoleurs/bricolage - Content management and publishing system
  • exflickr/GodAuth - Authentication layer for web app tools
  • JJ/hoborg - A dieselpunk novel with Spanish-created robot hobos in a balcanized America at the beginning of the XX century
  • zigdon/xkcd-Bucket - Bucket is the channel bot for #xkcd
  • jollyjinx/ZFS-TimeMachine - TimeMachine style backup for ZFS
  • atomia/atomiadns - Atomia DNS
  • comotion/VSF - Varnish Security Firewall
  • bgcngm/mtk-tools - Unpack / repack MT65xx/MT83xx boot.img, recovery.img or logo.bin
  • windytan/redsea - Decoder for FM-RDS.
  • tudorconstantin/Mojolicious-Boilerplate - The Web in an Awesome Box
  • openresty/lua-upstream-nginx-module - Nginx C module to expose Lua API to ngx_lua for Nginx upstreams
  • openresty/test-nginx - Data-driven test scaffold for Nginx C module and OpenResty Lua library development
  • mndrix/merge-this - Revision control stress tests
  • brendangregg/HeatMap - Heat map generation tools
  • crucially/riakfuse - Filesystem backed by riak
  • DmitryKoterov/dklab_realsync - dkLab RealSync: replicate developer's files over SSH in realtime
  • xme/pastemon - pastebin.com Content Monitoring Tool
  • ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/35432/mummer4-a-fast-and-versatile-genome-alignment-system Sat, 03 Feb 2018 04:59:17 -0600 https://bioinformaticsonline.com/bookmarks/view/35432/mummer4-a-fast-and-versatile-genome-alignment-system <![CDATA[MUMmer4: A fast and versatile genome alignment system]]> MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes; 

    Address of the bookmark: https://mummer4.github.io/

    ]]>     Jit