========
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: `GitHub` `<https://github.com/cancerit/ascatNgs>`_
:Article: `PNAS` `<https://www.pnas.org/doi/full/10.1073/pnas.1009843107/>`_
:Version: `4.5.0`

bcftools
~~~~~~~~
:Source code: `GitHub` `<https://github.com/samtools/bcftools>`_
:Article: `Bioinformatics` `<https://pubmed.ncbi.nlm.nih.gov/21903627/>`_
:Version: `>1.9`

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: `0.7.15`

cnvkit
~~~~~~
:Source code: `GitHub` `<https://github.com/etal/cnvkit>`_
:Article: `PLOS Computational Biology` `<http://dx.doi.org/10.1371/journal.pcbi.1004873>`_
:Version: `0.9.4`

csvkit
~~~~~~
:Source code: `GitHub` `<https://github.com/wireservice/csvkit>`_
:Article: `-`
:Version: `1.0.4`

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`

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: `100.2`

fastp
~~~~~
:Source code: `GitHub` `<https://github.com/OpenGene/fastp>`_
:Article: `Bioinformatics` `<https://doi.org/10.1093/bioinformatics/bty560>`_
:Version: `0.20.1`

fastqc
~~~~~~
:Source code: `GitHub` `<https://github.com/s-andrews/FastQC>`_
:Article: `Babraham` `<http://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`

manta
~~~~~
:Source code: `GitHub` `<https://github.com/Illumina/manta>`_
:Article: `Bioinformatics` `<https://doi.org/10.1093/bioinformatics/btv710>`_
:Version: `1.6.0`

multiqc
~~~~~~~
:Source code: `GitHub` `<https://github.com/ewels/MultiQC>`_
:Article: `Bioinformatics` `<http://dx.doi.org/10.1093/bioinformatics/btw354>`_
:Version: `1.11`

mosdepth
~~~~~~~~
:Source code: `GitHub` `<https://github.com/brentp/mosdepth>`_
:Article: `Bioinformatics` `<https://academic.oup.com/bioinformatics/article/34/5/867/4583630?login=true>`_
:Version: `0.2.9`

picard
~~~~~~
:Source code: `GitHub` `<https://github.com/broadinstitute/picard>`_
:Article: `-`
:Version: `2.25.0`

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: `1.12`

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: `GitHub` `<https://github.com/samtools/tabix>`_
:Article: `Bioinformatics` `<https://academic.oup.com/bioinformatics/article/27/5/718/262743>`_
:Version: `0.2.6`

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: `0.7.1`