Table 5.1 (continued)
Bioconda
software
tool
Short description
Further information
minimap2
Experimental tool to find approximate
mapping positions between long sequences
https://github.com/lh3/minimap
perl
The Perl programming language interpreter http://www.perl.org/
perl-netssleay
Perl extension for using OpenSSL
http://metacpan.org/pod/Net::
SSLeay
picard
Java tools for working with NGS data in the
BAM format
http://broadinstitute.github.io/
picard/
readseq
Read & reformat biosequences, Java
command-line version
http://iubio.bio.indiana.edu/soft/
molbio/readseq/java/
samtools
[11]
Tools for dealing with SAM, BAM and
CRAM files
https://github.com/samtools/
samtools
seqkit
Cross-platform and ultrafast toolkit for
FASTA/Q file manipulation
https://github.com/shenwei356/
seqkit
seqtk
Seqtk is a fast and lightweight tool for
processing sequences in the FASTA or
FASTQ format
https://github.com/lh3/seqtk
snpeff
Genetic variant annotation and effect
prediction toolbox
http://snpeff.sourceforge.net/
sra-tools
Retrieve raw data from NCBI-SRA;
download data files directly
https://github.com/ncbi/sra-tools
Star
Mapping RNA-Seq data. Splice aware
https://github.com/alexdobin/
STAR
subread
High-performance read alignment,
quantification, and mutation discovery
http://subread.sourceforge.net/
trimmomatic A flexible read trimming tool for Illumina
NGS data
http://www.usadellab.org/cms/?
page¼trimmomatic
vt
A tool set for manipulating and generating
VCF files
https://genome.sph.umich.edu/
wiki/Vt
wget
Free utility for non-interactive download of
files from the Web
https://www.gnu.org/software/
wget/manual/wget.html
Other essential/ helpful software tools
R and
RStudio
Statistical analysis program
https://www.rstudio.com/
Homer [12]
Basic ChIP Seq analysis: finding peaks/
regions; genome annotation of peaks;
functional annotation; Motif finding, etc.
http://homer.ucsd.edu/homer/
GSEA
[13, 14]
Gene Set Enrichment Analysis
http://software.broadinstitute.org/
gsea/index.jsp
GREAT
Function prediction of cis-regulatory
regions
http://great.stanford.edu/public/
html/index.php
(continued)
5 Computer Setup
65
Bioconda
software
tool
Short description
Further information
minimap2
Experimental tool to find approximate
mapping positions between long sequences
https://github.com/lh3/minimap
perl
The Perl programming language interpreter http://www.perl.org/
perl-netssleay
Perl extension for using OpenSSL
http://metacpan.org/pod/Net::
SSLeay
picard
Java tools for working with NGS data in the
BAM format
http://broadinstitute.github.io/
picard/
readseq
Read & reformat biosequences, Java
command-line version
http://iubio.bio.indiana.edu/soft/
molbio/readseq/java/
samtools
[11]
Tools for dealing with SAM, BAM and
CRAM files
https://github.com/samtools/
samtools
seqkit
Cross-platform and ultrafast toolkit for
FASTA/Q file manipulation
https://github.com/shenwei356/
seqkit
seqtk
Seqtk is a fast and lightweight tool for
processing sequences in the FASTA or
FASTQ format
https://github.com/lh3/seqtk
snpeff
Genetic variant annotation and effect
prediction toolbox
http://snpeff.sourceforge.net/
sra-tools
Retrieve raw data from NCBI-SRA;
download data files directly
https://github.com/ncbi/sra-tools
Star
Mapping RNA-Seq data. Splice aware
https://github.com/alexdobin/
STAR
subread
High-performance read alignment,
quantification, and mutation discovery
http://subread.sourceforge.net/
trimmomatic A flexible read trimming tool for Illumina
NGS data
http://www.usadellab.org/cms/?
page¼trimmomatic
vt
A tool set for manipulating and generating
VCF files
https://genome.sph.umich.edu/
wiki/Vt
wget
Free utility for non-interactive download of
files from the Web
https://www.gnu.org/software/
wget/manual/wget.html
Other essential/ helpful software tools
R and
RStudio
Statistical analysis program
https://www.rstudio.com/
Homer [12]
Basic ChIP Seq analysis: finding peaks/
regions; genome annotation of peaks;
functional annotation; Motif finding, etc.
http://homer.ucsd.edu/homer/
GSEA
[13, 14]
Gene Set Enrichment Analysis
http://software.broadinstitute.org/
gsea/index.jsp
GREAT
Function prediction of cis-regulatory
regions
http://great.stanford.edu/public/
html/index.php
(continued)
5 Computer Setup
65