Add full IVar processing steps for amplicon data

nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

https://nf-co.re/viralrecon

MIT License

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Add full IVar processing steps for amplicon data #42

Closed drpatelh closed 4 years ago

drpatelh commented 4 years ago

It makes sense to implement the extensive functionality offered by IVar to get from aligned BAM to consensus sequence. Varscan 2 and BCFTools can still be used for metagenomics data too. We are currently only using it to trim primer sequences so would need to add the other commands as described in the MANUAL.

Also, need to make sure that the parameters we use are applicable to Illumina data too.

drpatelh commented 4 years ago

Found this great resource too: https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/BFX-UT_ARTIC_Illumina

drpatelh commented 4 years ago

Initial implementation added here https://github.com/nf-core/viralrecon/pull/44