Tools and software

BALSAMIC ( version = 15.0.1 ) 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.

ascatNgs

Source code:

GitHub https://github.com/cancerit/ascatNgs

Article:

PNAS https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097604/

Version:

4.5.0

bcftools

Source code:

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

Article:

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

Version:

>=1.10

bedtools

Source code:

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

Article:

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

Version:

2.30.0

bwa

Source code:

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

Article:

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

Version:

0.7.17

cadd

Source code:

GitHub https://github.com/kircherlab/CADD-scripts/

Article:

Nature Genetics https://dx.doi.org/10.1038/ng.2892

Version:

1.6

cnvkit

Source code:

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

Article:

PLOS Computational Biology https://doi.org/10.1371/journal.pcbi.1004873

Version:

0.9.9

cnvpytor

Source code:

GitHub <https://github.com/abyzovlab/CNVpytor/>

Article:

GigaSciences <https://doi.org/10.1093/gigascience/giab074>

Version:

1.3.1

delly

Source code:

GitHub https://github.com/dellytools/delly

Article:

Bioinformatics https://academic.oup.com/bioinformatics/article/28/18/i333/245403

Version:

1.0.3

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:

104.3

fastp

Source code:

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

Article:

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

Version:

0.23.2

fastqc

Source code:

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

Article:

Babraham https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Version:

0.11.9

gatk

Source code:

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

Article:

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

Version:

3.8

genmod

Source code:

Github https://github.com/Clinical-Genomics/genmod

Version:

0.2.16

manta

Source code:

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

Article:

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

Version:

1.6.0

mosdepth

Source code:

GitHub https://github.com/brentp/mosdepth

Article:

Bioinformatics https://doi.org/10.1093/bioinformatics/btx699

Version:

0.3.3

multiqc

Source code:

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

Article:

Bioinformatics https://doi.org/10.1093/bioinformatics/btw354

Version:

1.12

picard

Source code:

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

Article:

-

Version:

2.27.1

sambamba

Source code:

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

Article:

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

Version:

0.8.2

samtools

Source code:

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

Article:

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

Version:

>1.11

sentieon-tools

Source code:

Commercial Tool https://www.sentieon.com/

Article:

Bioinformatics https://www.biorxiv.org/content/10.1101/115717v2

Version:

202010.02

somalier

Source code:

Github https://github.com/brentp/somalier

Article:

Genome Medicine https://doi.org/10.1186/s13073-020-00761-2

Version:

0.2.16

svdb

Source code:

Github https://github.com/J35P312/SVDB

Article:

F1000Res https://pubmed.ncbi.nlm.nih.gov/28781756/

Version:

2.8.1

tabix

Source code:

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

Article:

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

Version:

>=1.11

tiddit

Source code:

Github https://github.com/SciLifeLab/TIDDIT

Article:

F1000Res https://pubmed.ncbi.nlm.nih.gov/28781756/

Version:

3.3.2

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

vcfanno

Source code:

GitHub https://github.com/brentp/vcfanno

Article:

Genome Biology https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5/

Version:

0.3.3

vcf2cytosure

Source code:

GitHub https://github.com/NBISweden/vcf2cytosure

Article:

-

Version:

0.8