Closed thejmazz closed 8 years ago
nice looks good to me, I like the blog post idea for sharing what you learn as you go
also we should consult @andrewosh on workflow/pipeline systems in general at some point!
@maxogden @bmpvieira @mafintosh @yannickwurm
My end of week 1 recap:
khmer
, and its not just running the code, but also reading up on the tool and trying to understand the algorithm it uses, pros/cons, etc); having done that I think I can get makefile+snakemake done tmr for sure, maybe nextflow too, and then a day to write a complete post. I had hoped to have a blog post comparing a simple variant calling workflow tonight.bwa
, bowtie2
, soap3
, k-mer based methods) and different workflows (de novo assembly, read mapping, rare variants vs. GWAS). Still need to improve an understanding of which algorithms are best in what cases, but I think this can really only come with time. (And also with a workflow engine that facilitates easy swapping of tools and ability to compare results vs. bash script ;) )
Goal Become comfortable working with variant calling (VC) pipelines across various workflow systems.
Deliverables
Metrics and Targets