Public Repository

Last pushed: 4 months ago
Short Description
A collection of Bioinformatic and statistical tools
Full Description

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
Docker Pull Command
Owner
fischuu