What analyses should be run on the various states of assembly.

[mahesh-panchal]

IPA produces:

• *.purged.haplotigs.fasta
• *.purged.primary.fasta

HiFi asm produces:

• *.bp.hap1.p_ctg.{fasta,gfa}
• *.bp.hap2.p_ctg.{fasta,gfa}
• *.bp.p_ctg.{fasta,gfa}
• *.bp.p_utg.gfa
• *.bp.r_utg.gfa

What analyses should we be running on which files?

Quast, Busco, Blobtools, Merqury, Inspector [ *.bp.p_ctg.fasta, *.purged.primary.fasta ] Bandage [ *.bp.p_ctg.gfa ] Merqury [ *.bp.hap1.p_ctg.fasta+*.bp.hap2.p_ctg.fasta ] ?

Inspector is still being evaluated, but for now we'll include it anyway.

@iggyB What are you currently running on these outputs? @aersoares81 Any other opinions on what we should be analyzing here.

What should we be doing with the haplotigs and unitigs?

[iggyB]

@mahesh-panchal your list covers well current tools used for assembly QC on our site. In addition I sometimes check content of r_utg.

We could do some testing of purge_dups by using HiFi data and Omni-C data. Perhaps it would make sense to do manual run after each assembly. But as said previously, we can make decisions after kmer analysis and BUSCO.

[aersoares81]

(gosh, I'm late to this) I think it pretty much covers it, except we could replace Quast with our own stats scrips that we use pre-annotation.

[mahesh-panchal]

What's in the annotation scripts that is not in Quast? Quast also produces some nice plots and is also compatible with MultiQC. I'd like to be able to make a single report at the end of a run, so it's all in one place.

[mahesh-panchal]

@iggyB What do you mean by:

In addition I sometimes check content of r_utg.

What are you checking for in the unitig graph? Trimmed sequence?