fischuu/bitools repository overview

Tools currently available:

Basic image: ubuntu:16.04

Bandage 0.8.1 http://rrwick.github.io/Bandage/⁠ bcftools 1.3.1 http://www.htslib.org/download/⁠ BEDtools 2.26.0 http://bedtools.readthedocs.io/en/latest/index.html#⁠ BWA 0.7.15 https://sourceforge.net/projects/bio-bwa/files/⁠ Cufflinks 2.2.1 http://cole-trapnell-lab.github.io/cufflinks/install/⁠ Diamond 0.8.38 https://github.com/bbuchfink/diamond⁠ FastQC 0.11.5 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠ FEELnc 0.1.0 https://github.com/tderrien/FEELnc⁠ HiSAT2 2.0.5 https://ccb.jhu.edu/software/hisat2/index.shtml⁠ HTSlib 1.3.1 http://www.htslib.org/download/⁠ (includes bgzip, htsfile, tabix) MegaHit 1.1.2 https://github.com/voutcn/megahit⁠ Paladin 1.4.0 https://github.com/twestbrookunh/paladin/releases⁠ PEAR 0.9.10 https://sco.h-its.org/exelixis/web/software/pear/⁠ Picard 2.9.2 https://github.com/broadinstitute/picard/releases⁠ R 3.2.3 http://www.r-project.org⁠ samtools 1.3.1 http://www.htslib.org/download/⁠ selscan 1.2.0 https://github.com/szpiech/selscan⁠ seqtk 1.2 https://github.com/lh3/seqtk⁠ SRA Toolkit 2.8.2-1 https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software⁠ SPAdes 3.11.0 http://bioinf.spbau.ru/en/spades⁠ (with METASPAdes) SOAP 2.0.4 https://github.com/aquaskyline/SOAPdenovo2⁠ STAR 2.5.2b: https://github.com/alexdobin/STAR⁠ StringTie 1.33 https://ccb.jhu.edu/software/stringtie/⁠ Subread 1.5.3 (with Subjunc and featureCounts) http://bioinf.wehi.edu.au/subread-package/⁠ Sweed 3.3.2 (http://pop-gen.eu/wordpress/software/sweed⁠) TransDecoder v3.0.1 https://github.com/TransDecoder/TransDecoder⁠ Trimmomatic 0.36 http://www.usadellab.org/cms/?page=trimmomatic⁠ VCFtools 0.1.14 https://github.com/vcftools/vcftools/releases⁠ velvet 1.2.10 https://www.ebi.ac.uk/~zerbino/velvet/⁠

Bash tools: c/c++ compiler (gcc) OpenJDK 8 python pigz (parallel version of gzip)

Under development/Need to be added still GenomeBrowser (Struggling with X-Server access) GATK Beagle MultiQC R / RStudio

⁠UPDATES:

VERSION 0.1.11

• MegaHit 1.1.2 added
• SOAPdenovo2 added

VERSION 0.1.10

• selscan 1.2.0 added
• SweeD 3.3.2 added

VERSION 0.1.9

• SPAdes added
• velvet is now compiled with MAXKMERLENGTH=31 (instead of 127)

VERSION 0.1.8

• Bandage added

VERSION 0.1.7

• velvet added

VERSION 0.1.6

• FEELnc 0.1.0 added

VERSION 0.1.5

• Subreads (with Subjunc, featureCounts) 1.5.3 added

VERSION 0.1.4

• SAR Toolkit 2.8.2-1 added
• pigz for bash added

VERSION 0.1.3

• seqtk 1.2 added

VERSION 0.1.2

• Picard 2.9.2 added
• Trimmomatic 0.36 added
• Paladin 1.4.0 added

VERSION 0.1.1

• Diamond 0.8.4 added

VERSION 0.1

• Initial submission