Workflow¶
BALSAMIC ( version = 8.2.9 ) 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:
- Article:
- Version:
4.5.0
bcftools¶
- Source code:
- Article:
Bioinformatics https://pubmed.ncbi.nlm.nih.gov/21903627/
- Version:
>1.9
bedtools¶
- Source code:
- 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:
0.7.15
cnvkit¶
- Source code:
- Article:
PLOS Computational Biology http://dx.doi.org/10.1371/journal.pcbi.1004873
- Version:
0.9.4
csvkit¶
- Source code:
- Article:
-
- Version:
1.0.4
delly¶
- Source code:
- Article:
Bioinformatics https://academic.oup.com/bioinformatics/article/28/18/i333/245403
- Version:
0.8.7
ensembl-vep¶
- Source code:
- Article:
Genome Biology https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0974-4
- Version:
100.2
fastp¶
- Source code:
- Article:
Bioinformatics https://doi.org/10.1093/bioinformatics/bty560
- Version:
0.20.1
fastqc¶
- Source code:
- Article:
Babraham http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- Version:
0.11.9
gatk¶
- Source code:
- Article:
Current Protocols in Bioinformatics https://pubmed.ncbi.nlm.nih.gov/25431634/
- Version:
3.8
manta¶
- Source code:
- Article:
Bioinformatics https://doi.org/10.1093/bioinformatics/btv710
- Version:
1.6.0
multiqc¶
- Source code:
- Article:
Bioinformatics http://dx.doi.org/10.1093/bioinformatics/btw354
- Version:
1.11
mosdepth¶
- Source code:
- Article:
Bioinformatics https://academic.oup.com/bioinformatics/article/34/5/867/4583630?login=true
- Version:
0.2.9
picard¶
- Source code:
- Article:
-
- Version:
2.25.0
sambamba¶
- Source code:
- Article:
Bioinformatics https://pubmed.ncbi.nlm.nih.gov/25697820/
- Version:
0.6.6
samtools¶
- Source code:
- Article:
Bioinformatics https://pubmed.ncbi.nlm.nih.gov/19505943/
- Version:
1.12
sentieon-tools¶
- Source code:
Commercial Tool https://www.sentieon.com/
- Article:
Bioinformatics https://www.biorxiv.org/content/10.1101/115717v2
- Version:
202010.02
tabix¶
- Source code:
- Article:
Bioinformatics https://academic.oup.com/bioinformatics/article/27/5/718/262743
- Version:
0.2.6
vardict¶
- Source code:
- Article:
Nucleic Acid Research https://pubmed.ncbi.nlm.nih.gov/27060149/
- Version:
2019.06.04
vcfanno¶
- Source code:
- Article:
Genome Biology https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5/
- Version:
0.3.3
vcf2cytosure¶
- Source code:
- Article:
-
- Version:
0.7.1