BOL: Related items

Awesome perl frameworks, libraries and software - PART 5

Neel — Fri, 07 Jul 2017 04:12:47 -0500

robelix/sub2srt - subtitle converter
reyjrar/graphite-scripts - A Collections of Scripts for Working with Graphite
regilero/check_nginx_status - Nagios check for nginx status report
omniti-labs/resmon - resmon
motemen/App-htmlcat - redirect stdin to web browser
moose/Moo - Minimalist Object Orientation (with Moose compatibility)
miyagawa/fastpass - Tiny, XS free, standalone and preforking FastCGI daemon for PSGI
miyagawa/Filesys-Notify-Simple - Simple and dumb file system watcher
mhop/fhem-mirror - Branch 'master' is a read-only-mirror of svn://svn.code.sf.net/p/fhem/code which is updated once a day. On branch 'enocean' I am going to add some Enocean-Devices
lopnor/Plack-App-DAV - simple DAV server for Plack
kazuho/url_compress - a static PPM-based URL compressor / decompressor
jnthn/6model - Just a place that I'm keeping some meta-model prototyping; anything that matters will make it to another repo (e.g. nqp-rx one or Rakudo one) at some point.
jasonhancock/nagios-puppetdb - Nagios plugins and pnp4nagios templates related to Puppetlab's PuppetDB project.
goccy/p5-Compiler-Parser - Create Abstract Syntax Tree for Perl5
cgutteridge/Grinder - Create RDF data from spreadsheets or CSV
c9s/Plack-Middleware-OAuth - Plack Middleware for OAuth1 and OAuth2
bzip2-cuda/bzip2-cuda - Parallel implementation of bzip2 using cuda
alanstevens/ChocoPackages - Chocolatey Nuget Packages
SoylentNews/slashcode - The slashcode repository for SoylentNews. The initial code base was uploaded as it appeared on Sourceforge as of the last commit in September 2009
Miserlou/XSS-Harvest - XSS Weaponization

getopts.pl file

Jit — Fri, 15 Jun 2018 04:43:03 -0500

SSPACE_longread complain for getopts.pl file.

To resolve this, download and have in SSPACED-Longreads folder.

Cheers :)

BioCodes/BioScripts

Jit — Tue, 22 Apr 2014 20:53:33 -0500

Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

Scripts

Jit — Wed, 30 Nov 2016 10:35:15 -0600

Useful script for NGS analysis.

Address of the bookmark: http://augustus.gobics.de/binaries/scripts/

Python Mini Projects !

BioStar — Mon, 16 Jan 2023 02:14:03 -0600

There is a directory for each chapter of the book. Each directory contains a test.py program you can use with pytest to check that you have written the program correctly. I have included a short README to describe each exercise. If you have problems writing code (or if you would like to support this project!), the book contains details about the skills you need.

https://github.com/kyclark/tiny_python_projects

Address of the bookmark: https://github.com/kyclark/tiny_python_projects

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

Neel — Sun, 03 Apr 2022 20:35:19 -0500

Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s internal score. Merfin increased the precision of genotyped calls in several benchmarks, improved consensus accuracy and reduced frameshift errors when applied to human and nonhuman assemblies built from Pacific Biosciences HiFi and continuous long reads or Oxford Nanopore reads, including the first complete human genome. Moreover, we introduce assembly quality and completeness metrics that account for the expected genomic copy numbers.

More at https://www.nature.com/articles/s41592-022-01445-y

Address of the bookmark: https://github.com/arangrhie/merfin

Convert VCF to tab-deilimited table

Seema Singh — Tue, 15 May 2018 07:39:08 -0500

Performed with GATK :

java -Xmx8g -jar GenomeAnalysisTK.jar \
-T VariantsToTable \
-R reference.fa \
-V reference_genomes_GT.vcf \
-F CHROM -F POS -F REF -F ALT -GF GT \
-o reference_genomes_GT.table
multiple_sample.vcf should also be converted to multiple_sample_GT.table using this approach.