Workflow

BALSAMIC ( version = 7.2.4 ) uses myriad of tools and softwares to analyze fastq files. This section covers why each one is included: usage and parameters, and relevant external links.

bcftools

Source code

GitHub <https://github.com/samtools/bcftools>

Article

Bioinformatics <https://pubmed.ncbi.nlm.nih.gov/21903627/>

Version

1.9.0

bedtools

Source code

GitHub <https://github.com/arq5x/bedtools2>

Article

Bioinformatics <https://pubmed.ncbi.nlm.nih.gov/20110278/>

Version

2.28.0

bwa

Source code

GitHub <https://github.com/lh3/bwa>

Article

Bioinformatics <https://arxiv.org/abs/1303.3997>

Version

0.7.15

cnvkit

Source code

GitHub <https://github.com/etal/cnvkit>

Article

PLOS Computational Biology <http://dx.doi.org/10.1371/journal.pcbi.1004873>

Version

0.9.4a0

csvkit

Source code

GitHub <https://github.com/wireservice/csvkit>

Article

-

Version

1.0.4

ensembl-vep

Source code

GitHub <https://github.com/Ensembl/ensembl-vep>

Article

Genome Biology <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4>

Version

99.1

fastp

Source code

GitHub <https://github.com/OpenGene/fastp>

Article

Bioinformatics <https://doi.org/10.1093/bioinformatics/bty560>

Version

0.20.0

fastqc

Source code

GitHub <https://github.com/s-andrews/FastQC>

Article

Babraham <http://www.bioinformatics.babraham.ac.uk/projects/fastqc/>

Version

0.11.5

gatk

Source code

Github <https://github.com/broadinstitute/gatk>

Article

Current Protocols in Bioinformatics <https://pubmed.ncbi.nlm.nih.gov/25431634/>

Version

3.8

manta

Source code

GitHub <https://github.com/Illumina/manta>

Article

Bioinformatics <https://doi.org/10.1093/bioinformatics/btv710>

Version

1.3.0

multiqc

Source code

GitHub <https://github.com/ewels/MultiQC>

Article

Bioinformatics <http://dx.doi.org/10.1093/bioinformatics/btw354>

Version

1.7

picard

Source code

GitHub <https://github.com/broadinstitute/picard>

Article

-

Version

2.17.0

sambamba

Source code

GitHub <https://github.com/biod/sambamba>

Article

Bioinformatics <https://pubmed.ncbi.nlm.nih.gov/25697820/>

Version

0.6.6

samtools

Source code

GitHub <https://github.com/samtools/samtools>

Article

Bioinformatics <https://pubmed.ncbi.nlm.nih.gov/19505943/>

Version

1.6

strelka

Source code

GitHub <https://github.com/Illumina/strelka>

Article

Nature Methods <https://www.nature.com/articles/s41592-018-0051-x/>

Version

2.8.4

tabix

Source code

GitHub <https://github.com/samtools/tabix>

Article

Bioinformatics <https://academic.oup.com/bioinformatics/article/27/5/718/262743>

Version

0.2.5

vardict

Source code

GitHub <https://github.com/AstraZeneca-NGS/VarDict>

Article

Nucleic Acid Research <https://pubmed.ncbi.nlm.nih.gov/27060149/>

Version

2019.06.04