winnowmap PacBio CCS alignment

[sjin09]

To whom it may concern,

I am writing to inquire whether the authors of the program had compared the results from winnowmap -ax map-pb and -ax asm20 bam file.

Minimap2 recommends using asm20 for mapping CCS reads and when I compared germline mutation results from asm5, asm10 and asm20 bam files, asm20 parameter performed the best for germline mutation calling. I was also wondering if there was reason for recommending the alternative parameter (map-pb) instead of the standard parameter (asm20)

winnowmap recommendation

winnowmap -W repetitive_k15.txt -ax map-pb ref.fa hifi.fq.gz > output.sam

minimap2 recommendation

./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio CCS genomic reads

Many thanks,

Regards,
Sangjin

[cjain7]

Although Winnowmap was started using minimap2 as base implementation, over the time I have made significant changes to the algorithm (particularly seeding and anchor chaining). It may be that asm20 works best for minimap2, but it didn't in Winnowmap. At our end, we were benchmarking for germline SV calling using SURVIVOR.

when I compared germline mutation results from asm5, asm10 and asm20 bam files, asm20 parameter performed the best for germline mutation calling.

I'd be really curious how winnowmap -W repetitive_k15.txt -ax map-pb performs on your benchmark. If you get chance, please let us know your observations. Winnowmap is designed particularly to target highly repetitive sequences (e.g., seg-dups, satellite arrays). A preprint will be out soon describing this.

[sjin09]

I will report back!

[sjin09]

I can report that winnowmap map_pb parameter is slightly better than minimap2 asm20 parameter for the somatic mutations I am attempting to detect!

[jelber2]

I think pbmm2 from PacBio uses something like this for the minimap2 preset for CCS reads

-k19 -w10 -O5,56 -E4,1 -A2 -B5 -z400,50 -r2000 \
--lj-min-ratio 0.5 -g5000

# see https://github.com/PacificBiosciences/pbmm2#what-are-parameter-sets-and-how-can-i-override-them