Comments (3)
This was initially added here #48
from viralrecon.
Hi @drpatelh
I have made little changes here and there and will create a PR soon.
Questions that came up in usage.md
:
Would it be possible to add a sentence to --amplicon_bed
and --amplicon_fasta
to say what it is needed for? Why is a bed file needed if we map the reads any way? Why is a fasta file needed if we assemble anyways? SOLVED - added some more description in the docs
Why are VarScan2
and iVar
used for variant calling of reads against the reference genome, and Minimap2
, seqwish
, vg
for variant calling of de-novo assemblies against the reference genome? Are the latter ones better suited for genome vs. genome? And why is specifically vg
failing? Does --run_vg
run specifically vg
, or Minimap2
and seqwish
as well? (I obviously don't know these tools yet and don't know about the concept of a variant graph yet)
Why is especially minia failing and hence not in the defaults for --assemblers
? - SOLVED - minia added back in as default
Questions that came up in output.md
:
Why are you using different trimming tools? fastp
for general adapter trimming, iVar trim
before variant calling, Cutadapt
before de-novo assembly. SOLVED - Elaborated a bit more in each section to make the distinction clearer
Best
Katrin
from viralrecon.
Docs are looking nice now as of #103
from viralrecon.
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from viralrecon.