Workflow

BALSAMIC ( version = 4.3.0 ) 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