Table 5.1 Bioinformatics related packages for Linux and Mac OS provided by Bioconda
Bioconda
software
tool
Short description
Further information
bamtools [1] C++ API & command-line toolkit for
working with BAM data
https://github.com/pezmaster31/
bamtools
bbmap
BBMap is a short-read aligner, as well as
various other bioinformatic tools
https://sourceforge.net/projects/
bbmap
BCFtools
[2, 3]
BCFtools is a set of utilities that manipulate
variant calls in the Variant Call Format
(VCF)
https://github.com/samtools/
bcftools
BEDTools
[4, 5]
A powerful toolset for genome arithmetic
http://bedtools.readthedocs.org/
bioawk
BWK awk modified for biological data
https://github.com/lh3/bioawk
blast
BLAST+ is a new suite of BLAST tools that
utilizes the NCBI C++ Toolkit
http://blast.ncbi.nlm.nih.gov
bowtie2 [6]
Fast and sensitive read alignment
Mapping MCiP/ChIP-Seq data
http://bowtie-bio.sourceforge.net/
bowtie2/index.shtml
bwa [7, 8]
The BWA read mapper
https://github.com/lh3/bwa
cutadapt
Trim adapters from high-throughput
sequencing reads
https://cutadapt.readthedocs.io/
datamash
GNU Datamash is a command-line program
which performs basic numeric, textual and
statistical operations on input textual data
files
http://www.gnu.org/software/
datamash
Emboss [9]
The European Molecular Biology Open
Software Suite
http://emboss.open-bio.org/
entrez-direct Entrez Direct (EDirect) is an advanced
method for accessing the NCBI’s set of
interconnected databases (publication,
sequence, structure, gene, variation,
expression, etc.) from a Linux/Unix
terminal window
ftp://ftp.ncbi.nlm.nih.gov/entrez/
entrezdirect/versions/13.3.
20200128/README
fastqc
A quality control tool for high-throughput
sequence data
http://www.bioinformatics.
babraham.ac.uk/projects/fastqc/
freebayes
Bayesian haplotype-based polymorphism
discovery and genotyping
https://github.com/ekg/freebayes
control-freec Copy number and genotype annotation
from whole genome and whole exome
sequencing data
https://github.com/BoevaLab/
FREEC
hisat2 [10]
Graph-based alignment of next-generation
sequencing reads to a population of
genomes
https://ccb.jhu.edu/software/hisat2/
index.shtml
htslib
C library for high-throughput sequencing
data formats
https://github.com/samtools/htslib
(continued)
64
M. Kappelmann-Fenzl
Bioconda
software
tool
Short description
Further information
bamtools [1] C++ API & command-line toolkit for
working with BAM data
https://github.com/pezmaster31/
bamtools
bbmap
BBMap is a short-read aligner, as well as
various other bioinformatic tools
https://sourceforge.net/projects/
bbmap
BCFtools
[2, 3]
BCFtools is a set of utilities that manipulate
variant calls in the Variant Call Format
(VCF)
https://github.com/samtools/
bcftools
BEDTools
[4, 5]
A powerful toolset for genome arithmetic
http://bedtools.readthedocs.org/
bioawk
BWK awk modified for biological data
https://github.com/lh3/bioawk
blast
BLAST+ is a new suite of BLAST tools that
utilizes the NCBI C++ Toolkit
http://blast.ncbi.nlm.nih.gov
bowtie2 [6]
Fast and sensitive read alignment
Mapping MCiP/ChIP-Seq data
http://bowtie-bio.sourceforge.net/
bowtie2/index.shtml
bwa [7, 8]
The BWA read mapper
https://github.com/lh3/bwa
cutadapt
Trim adapters from high-throughput
sequencing reads
https://cutadapt.readthedocs.io/
datamash
GNU Datamash is a command-line program
which performs basic numeric, textual and
statistical operations on input textual data
files
http://www.gnu.org/software/
datamash
Emboss [9]
The European Molecular Biology Open
Software Suite
http://emboss.open-bio.org/
entrez-direct Entrez Direct (EDirect) is an advanced
method for accessing the NCBI’s set of
interconnected databases (publication,
sequence, structure, gene, variation,
expression, etc.) from a Linux/Unix
terminal window
ftp://ftp.ncbi.nlm.nih.gov/entrez/
entrezdirect/versions/13.3.
20200128/README
fastqc
A quality control tool for high-throughput
sequence data
http://www.bioinformatics.
babraham.ac.uk/projects/fastqc/
freebayes
Bayesian haplotype-based polymorphism
discovery and genotyping
https://github.com/ekg/freebayes
control-freec Copy number and genotype annotation
from whole genome and whole exome
sequencing data
https://github.com/BoevaLab/
FREEC
hisat2 [10]
Graph-based alignment of next-generation
sequencing reads to a population of
genomes
https://ccb.jhu.edu/software/hisat2/
index.shtml
htslib
C library for high-throughput sequencing
data formats
https://github.com/samtools/htslib
(continued)
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M. Kappelmann-Fenzl