<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36533?offset=460 https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing Thu, 04 Oct 2018 05:23:59 -0500 https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing <![CDATA[nQuire: a statistical framework for ploidy estimation using next generation sequencing]]> nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data Tue, 27 Nov 2018 04:43:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data <![CDATA[lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data]]> lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

 

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

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data Tue, 22 Jan 2019 06:26:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38762/katuali-is-a-flexible-consensus-pipeline-implemented-in-snakemake-to-basecall-assemble-and-polish-oxford-nanopore-technologies-sequencing-data <![CDATA[Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data]]>
  • Run a pipeline processing fast5s to a consensus in a single command.
  • Recommended fixed "standard" and "fast" pipelines.
  • Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
  • Seemless distribution of tasks over local or distributed compute.
  • Highly configurable.
  • Open source (Mozilla Public License 2.0).

    • Documentation can be found at https://nanoporetech.github.io/katuali/.

    Address of the bookmark: https://github.com/nanoporetech/katuali

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data Thu, 28 May 2020 21:57:03 -0500 https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data <![CDATA[Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data]]> Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

    Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.

    Address of the bookmark: https://github.com/dnanexus/parliament2

    ]]>     Jit     https://bioinformaticsonline.com/pages/view/7986/list-of-bioinformatics-open-source-projectssoftware Tue, 21 Jan 2014 14:28:37 -0600 https://bioinformaticsonline.com/pages/view/7986/list-of-bioinformatics-open-source-projectssoftware <![CDATA[List of bioinformatics open source projects/software.]]> Open source software is software that can be freely used, changed, and shared (in modified or unmodified form) by anyone. Open source software is made by many people, and distributed under licenses that comply with the Open Source Definition.The Open Source Initiative (OSI) is a global non-profit that supports and promotes the open source movement. Followings are the OS bioinformatics projects/software :

    .NET Bio

    http://blogs.msdn.com/b/msr_er/archive/2011/10/18/microsoft-biology-foundation-evolves-into-new-toolkit-net-bio.aspx

    A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists.

    AMPHORA ("AutoMated Phylogenomic infeRence Application")

    http://wolbachia.biology.virginia.edu/WuLab/Software.html

    Metagenomics analysis software

    Anduril

    http://www.anduril.org/anduril/site/

    Component-based workflow framework for data analysis

    Armadillo workflow platform

    Tool for designing and executing phylogenetic workflows

    AutoDock

    http://autodock.scripps.edu/

    suite of automated docking tools

    Biochemical Algorithms Library (BALL)

    http://www.ball-project.org/

    C++ library and framework for molecular modeling and visualization designed for rapid prototyping

    Bio4j

    http://bio4j.com/

    Bio4j is a bioinformatics platform and graph based database built around most data available in UniProt KB(Swiss-Prot + TrEMBL), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB

    Bioclipse

    www.bioclipse.net

    Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).

    Bioconductor

    http://www.bioconductor.org/

    R (programming language) language toolkit

    Bioinformatics Learning Tutorial (BLT)

    http://sourceforge.net/projects/biotutorial/

    Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation

    BioHaskell

    http://biohaskell.org/

    Haskell (programming language)

    BioJava

    http://biojava.org/wiki/Main_Page

    Java (programming language)

    BioMOBY

    http://biomoby.org/

    registry of web services

    BioPerl

    http://www.bioperl.org/wiki/Main_Page

    Perl language toolkit

    BioPHP

    http://www.biophp.org/

    PHP language toolkit

    Biopython

    http://biopython.org/wiki/Main_Page

    Python language toolkit

    BioRails

    https://github.com/biorails

    a data management system designed to support researchers in drug discovery

    BioRuby

    http://bioruby.org/

    Ruby language toolkit

    BioSmalltalk

    https://code.google.com/p/biosmalltalk/

    Smalltalk language toolkit

    BioUno

    http://www.biouno.org/

    BioUno is a project that applies Continuous Integration tools and techniques in Bioinformatics. It uses Jenkins and its plug-in API to create biology workflows and manage computer clusters.

    caCORE

     

    ontologic representation environment

    caArray

    https://cabig-stage.nci.nih.gov/community/tools/caArray

    ontologic representation environment

    EMBOSS

    http://emboss.sourceforge.net/

    Suite of packages for sequencing, searching, etc.

    Gaggle

    https://www.gaggle.net/

    A framework for interoperability between systems biology software

    Galaxy

    http://galaxyproject.org/

    Scientific workflow and data integration system

    GenePattern

    http://www.broadinstitute.org/cancer/software/genepattern/

    Scientific workflow system that provides access to more than 150 genomic analysis tools

    GeWorkbench

    http://wiki.c2b2.columbia.edu/workbench/index.php/Home

    Genomic data integration platform

    GMOD

    http://www.gmod.org/wiki/Main_Page

    Toolkit for addressing many common challenges at biological databases.

    GeneProf

    http://www.geneprof.org/GeneProf/

    A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq.

    GeneTalk

    http://www.gene-talk.de/

    Tool for filtering sequence variants in VCF files. Network for scientists and clinicians for expertise and knowledge exchange. Database of annotations aboute sequence variants with clinically relevant information.

    GenGIS

    http://kiwi.cs.dal.ca/GenGIS/Main_Page

    Application that allows users to combine digital map data with information about biological sequences collected from the environment.

    GenomeSpace

    http://www.genomespace.org/

    Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools

    GENtle

    http://directory.fsf.org/wiki/GENtle

    An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files

    Integrated Genome Browser

    http://bioviz.org/igb/

    Java-based desktop genome browser

    Integrative Genomics Viewer (IGV)

    http://www.broadinstitute.org/igv/

    High-performance desktop tool for interactive visual exploration of diverse genomic data

    IntAct

    http://www.ebi.ac.uk/intact/

    molecular interaction database

    InterMine

    http://intermine.github.io/intermine.org/

    Extensive data warehouse system for the analysis and integration of biological datasets

    Java Treeview

    http://jtreeview.sourceforge.net/

    microarray data viewer

    LabKey Server

    http://labkey.com/

    platform for integrating, analyzing and sharing data

    OpenClinica

    https://www.openclinica.com/

    software for capturing and managing data in clinical trials

    PromKappa

    http://xbioinformatics.wordpress.com/tag/promkappa/

    PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis.

    MeV: Multi-Experiment Viewer

    http://www.tm4.org/mev.html

    a desktop application for the analysis, visualization and data-mining of large-scale genomic data

    PathVisio

    http://www.pathvisio.org/

    a desktop software for drawing, analysis and visualization of biological pathways

    REDCRAFT

    software for determining tertiary protein structure given assigned Residual Dipolar Coupling data

    SAM Tools

    Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments

    Staden Package

    Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin.

    STAMP

    Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results.

    supraHex

    An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map

    Taverna workbench

    Tool for designing and executing workflows

    TGAC Browser

    Genome Browser, visualisation solutions for big data in the genomic era

    T-REX WebServer

    Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models)

    UGENE

    integrated bioinformatics tools

    Visomics

    bioinformatics tools for omics data

    Genome Analysis Toolkit 1.0 (GATK 1.0)

    a software package to analyse next-generation resequencing data

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/opportunity/view/24297/bioinformatics-walkin-at-nii Fri, 04 Sep 2015 21:48:15 -0500 <![CDATA[Bioinformatics WalkIn at NII]]> ADVERTISEMENT OF WALK-IN-INTERVIEW

    NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only)

    DURATION : One Year

    NAME OF THE PROJECT : Next generation sequencing facility

    EDUCATIONAL QUALIFICATIONS : At least a Masters degree in Bioinformatics and Bachelors degree in any stream of life sciences

    REQUIREMENTS :

    Around 5 years of experience and proven track record in next generation sequence data analysis (supported by publications in peer-reviewed journals), ability to analyze transcriptomics, Chip-seq, and small RNA –seq data.

    : Should have the ability to analyze raw primary data generated by Illumina next generation sequencing platforms and create / troubleshoot custom analysis Pipelines.

    Should have ability to handle all downstream secondary and tertiary data analysis using commercially available as well as open source softwares (transcriptomics, ChIP-seq, small RNA-seq)

    Apart from these, the applicant should have knowledge of the following: Programming: Perl and Python. Operating system:

    Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cufflinks, AvadisNGS, CLC Genomics Workbench, Galaxy, BaseSpace, Trinity Statistics: Microsoft Excel and R. Database: MySQL Genome Browser: UCSC, Ensemble, IGV, IGB Motif Analysis Tools: MEME Suite, Transfac and RSAT Functional Annotation Tools: DAVID, GeneCodis, Gene Cards Networking Tools: Cytoscape

    EMOLUMENTS : The incumbent will be paid a fee of Rs. 2000/- per sitting/ per day.

    SCIENTIST NAME : Dr. Arnab Mukhopadhyay,

    Staff Scientific V Next generation sequencing facility

    SCIENTIST’S E-MAIL ID : arnab@nii.ac.in

    WALK IN INTERVIEW ON : 18th September, 2015

    REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

    PLEASE NOTE- 1. CANDIDATE MAY FILL UP APPLICATION IN THE PRECRIBED FORMAT ALONG WITH NECESSARY DOCUMENTS FOR VERIFICATION. 2. APPLICATIONS CONTAINING INCOMPLETE INFORMATION SHALL NOT BE ENTERTAINED. 3. DATE OF PASSING THE EXAMINATIONS MUST BE INDICATED CLEARLY. 4. ONLY REGISTERED CANDIDATES WILL BE INTERVIEWED. 5. NO TA/DA WILL BE PAID FOR ATTENDING THE INTERVIEW PRESCRIBED FORM 1. NAME 2. FATHER’S NAME 3. MOTHER’S NAME 4. DATE OF BIRTH 5. SEX (MALE/FEMALE) 6. CATEGORY (SC/ ST/ OBC/ PH) 7. ADDRESS a. (CORRSPONDENCE) b. (PERMANENT) 8. E MAIL, TELEPHONE NO. & MOBILE No (if any) 9. ACADEMIC & PROFESSIONAL QUALIFICATIONS NAME OF EXAMINATION PASSED WITH SUBJECTS YEAR OF PASSING BOARD/ UNIVERSITY PERCENTAGE/ DIVISION REMARKS 10. PAST EXPERIENCE & PRESENT EMPLOYMENT, IF ANY 11. CANDIDATES SHOULD STATE CLEARLY WHETHER THEY HAVE BEEN AWARDED PH.D DEGREE OR THESIS HAS BEEN SUBMITTED. 12. HAVE YOU APPLIED FOR A POSITION EARLIER IN THE INSTITUTE? IF SO:- (1) THE DETAILS OF THE PROJECT AND PROJECT INVESTIGATOR (2) IF CALLED FOR INVERVIEW, RESULTS THEREOF

    More at http://www1.nii.res.in/sites/default/files/walkininterview-18sept2015.pdf

    ]]>         https://bioinformaticsonline.com/researchlabs/view/26828/bioinfolab Fri, 25 Mar 2016 11:05:35 -0500 <![CDATA[BioinfoLab]]> Laboratory of Statistics and Computational tools for Bioinformatics

    The Laboratory of Statistics and Computational tools for Bioinformatics (BioinfoLab) is hosted at the Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR . The laboratory has been officially opened in 2012 with the support of Programma Operativo Nazionale "Ricerca e Competitività" 2007-2013 (PON "R&C"), and it incorporates several expertise and research activities started since 2007, and supported by several CNR projects. Main interest of BioinfoLab is to develop novel statistical methods and computational tools for the analysis of high dimensional data arising from "Multi-omics" applications. In particular, current activities involve the analysis of ChIP-seq and RNA-seq experiments.

    More at http://bioinfo.na.iac.cnr.it/BioinfoLab/index.html

    ]]>         https://bioinformaticsonline.com/blog/view/42188/tools-and-method-for-haplotype-phasing Fri, 04 Sep 2020 20:41:40 -0500 https://bioinformaticsonline.com/blog/view/42188/tools-and-method-for-haplotype-phasing <![CDATA[Tools and Method for Haplotype phasing !]]> Huge amounts of genotype data are being produced with recent technological advances, both from increasingly  comprehensive and inexpensive genome-wide SNP microarrays and from ever more accessible whole-genome and whole-exome sequencing methods. The vast amount of knowledge contained in these results, however, is best  exploited through phased haplotypes, which classify the alleles co-located on the same chromosome. Since sequence and SNP array data normally take the form of unphased genotypes, one does not specifically observe which of the two parental chromosomes, or haplotypes, falls on a specific allele. Fortunately, new advances in both computational and laboratory methods promise improved determination of haplotype phase. Following are useful tools :
     

    Arlequin: http://cmpg.unibe.ch/software/arlequin3/

    BEAGLE: http://faculty.washington.edu/browning/beagle/beagle.html

    fastPHASE: http://stephenslab.uchicago.edu/software.html

    GENEHUNTER: http://linkage.rockefeller.edu/soft/gh/

    The Genome Analysis Toolkit:

    http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

    IMPUTE2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

    MACH: http://www.sph.umich.edu/csg/abecasis/MACH/

    MERLIN: http://www.sph.umich.edu/csg/abecasis/Merlin/

    PHASE: http://stephenslab.uchicago.edu/software.html

    PL-EM: http://www.people.fas.harvard.edu/~junliu/plem/

    “Read-backed phasing” algorithm: http://www.broadinstitute.org/gsa/wiki/index.php/Read-backed_phasing_algorithm

    SHAPE-IT: http://www.griv.org/shapeit/

    ]]>     Manisha Mishra     https://bioinformaticsonline.com/bookmarks/view/30336/finding-patterns-in-biological-sequences Thu, 22 Dec 2016 10:30:49 -0600 https://bioinformaticsonline.com/bookmarks/view/30336/finding-patterns-in-biological-sequences <![CDATA[Finding Patterns in Biological Sequences]]> In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly available tools and databases for pattern discovery. On-line supplement is available through http://genetics.uwaterloo.ca/∼tvinar/cs798g/motif.

    Address of the bookmark: http://engr.case.edu/li_jing/papers/00798gpattern.pdf

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 Mon, 10 Apr 2017 04:45:40 -0500 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 <![CDATA[WGS Celera Assembler version 8.3rc2]]> These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

    This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

    The source code package includes full source code (revision 4627), Makefiles, and scripts.  A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.  This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

    Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

    Interesting scripts within it

    urbe@urbo214b[bin] ls                                                        []
    -rwxrwxr-x 1 urbe urbe  11K Apr 10 11:41 addCNSToStore
    -rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs
    -rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest
    -rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds
    -rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta
    -rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics
    -rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl
    -rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr
    -rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart
    -rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus
    -rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness
    -rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap
    -rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs
    -rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs
    -rwxrwxr-x 1 urbe urbe  18K Apr 10 11:41 ca2ace.pl
    -rwxrwxr-x 1 urbe urbe  12K Apr 10 11:41 caqc_help.ini
    -rwxrwxr-x 1 urbe urbe  61K Apr 10 11:41 caqc.pl
    -rwxrwxr-x 1 urbe urbe  23K Apr 10 11:41 cat-corrects
    -rwxrwxr-x 1 urbe urbe  24K Apr 10 11:41 cat-erates
    -rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
    -rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump
    -rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera
    -rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply
    -rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise
    -rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat
    -rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl
    -rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 convertOverlap
    -rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA
    -rwxrwxr-x 1 urbe urbe  20K Apr 10 11:41 convertToPBCNS
    -rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags
    -rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps
    -rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio
    -rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns
    -rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate
    -rwxrwxr-x 1 urbe urbe  37K Apr 10 11:41 demotePosMap
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles
    -rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons
    -rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate
    -rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold
    -rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition
    -rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages
    -rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense
    -rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA
    -rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
    -rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
    -rwxrwxr-x 1 urbe urbe  62K Apr 10 11:40 fastqSimulate
    -rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort
    -rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA
    -rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
    -rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim
    -rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs
    -rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth
    -rwxrwxr-x 1 urbe urbe  29K Apr 10 11:41 fragsInVars
    -rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones
    -rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper
    -rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench
    -rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate
    -rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ
    -rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling
    -rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM
    -rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim
    -rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish
    -rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
    -rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique
    -rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy
    -rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl
    -rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim
    -rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply
    -rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl
    -rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses
    -rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds
    -rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout
    -rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore
    -rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition
    -rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats
    -rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
    -rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer
    -rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild
    -rwxrwxr-x 1 urbe urbe  33K Apr 10 11:41 overlapStoreIndexer
    -rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 overlapStoreSorter
    -rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry
    lrwxrwxrwx 1 urbe urbe    4 Apr 10 11:41 pacBioToCA -> PBcR
    -rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
    -rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon
    -rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns
    -rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment
    -rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
    -rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
    -rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
    -rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates
    -rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
    -rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
    -rwxrwxr-x 1 urbe urbe  88K Apr 10 11:41 runCA-dedupe
    -rwxrwxr-x 1 urbe urbe  14K Apr 10 11:41 runCA-overlapStoreBuild
    -rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh
    -rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
    -rwxrwxr-x 1 urbe urbe  13K Apr 10 11:40 show-corrects
    -rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs
    -rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator
    drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR
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    -rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracearchiveToCA
    -rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracedb-to-frg.pl
    -rwxrwxr-x 1 urbe urbe  44K Apr 10 11:41 trimFastqByQVWindow
    -rwxrwxr-x 1 urbe urbe  18K Apr 10 11:40 uidclient
    -rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
    -rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v8-to-v9
    -rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v9-to-v10
    -rwxrwxr-x 1 urbe urbe  854 Apr 10 11:41 utg2fasta
    -rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
    -rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix


    Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

    ]]>     Jit