Workflow¶

BALSAMIC ( version = 4.2.0 ) 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
Article:	Bioinformatics
Version:	`1.9.0`_

bedtools¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`2.28.0`_

bwa¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`0.7.15`_

cnvkit¶

Source code:	GitHub
Article:	PLOS Computational Biology
Version:	`0.9.4a0`_

csvkit¶

Source code:	GitHub
Article:	`-`_
Version:	`1.0.4`_

ensembl-vep¶

Source code:	GitHub
Article:	Genome Biology
Version:	`99.1`_

fastp¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`0.20.0`_

fastqc¶

Source code:	GitHub
Article:	Babraham
Version:	`0.11.5`_

gatk¶

Source code:	Github
Article:	Current Protocols in Bioinformatics
Version:	`3.8`_

manta¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`1.3.0`_

multiqc¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`1.7`_

picard¶

Source code:	GitHub
Article:	`-`_
Version:	`2.17.0`_

sambamba¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`0.6.6`_

samtools¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`1.6`_

strelka¶

Source code:	GitHub
Article:	Nature Methods
Version:	`2.8.4`_

tabix¶

Source code:	GitHub
Article:	Bioinformatics
Version:	`0.2.5`_

vardict¶

Source code:	GitHub
Article:	Nucleic Acid Research
Version:	`2019.06.04`_