Repo of Latch Bio workflows
First workflow is called snipflow.
The goal of this wf is to
- Download a genome file from genbank as fasta using efetch. Initially this will be used for viral genomes, using ebola as an example.
- Download a sequencing project from SRA of new ebola isolates to find variants, using fasterq-dump
- Align sequences using bwa
- Find variants usinf bcf tools
- Result in vcf file that can be loaded to IGV to visualize variants.
Above will be registered with latch bio as a workflow.
The basic command line code for this is based on code from the biostar handbook by Istvan Albert