Workflow
BALSAMIC ( version = 6.0.0 ) 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.
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 |
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 |