Workflow¶
BALSAMIC ( version = 8.0.1 ) 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.
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
Delly¶
- Source code
GitHub <https://github.com/dellytools/delly>
- Article
Bioinformatics <https://academic.oup.com/bioinformatics/article/28/18/i333/245403>
- Version
0.8.7