Workflow¶
BALSAMIC ( version = 4.2.1 ) 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 |
---|---|
Article: | Bioinformatics |
Version: | `1.9.0`_ |
bedtools¶
Source code: | GitHub |
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Article: | Bioinformatics |
Version: | `2.28.0`_ |
bwa¶
Source code: | GitHub |
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Article: | Bioinformatics |
Version: | `0.7.15`_ |
cnvkit¶
Source code: | GitHub |
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Article: | PLOS Computational Biology |
Version: | `0.9.4a0`_ |
ensembl-vep¶
Source code: | GitHub |
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Article: | Genome Biology |
Version: | `99.1`_ |
fastp¶
Source code: | GitHub |
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Article: | Bioinformatics |
Version: | `0.20.0`_ |
gatk¶
Source code: | Github |
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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`_ |
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`_ |