all-mapper for differently trimmed mates

Question

[Roye Rozov]

I am trying to map paired end reads to contigs I have assembled from a metagenome. I would like to keep all alignments up to some edit/hamming distance threshold, so I thought yara (formerly masai) would be good for this task. Unfortunately, when I try to index my contigs, I get the error message Maximum number of contigs exceeded.

Also, the reads I am mapping were trimmed to remove Illumina adapters and thus vary in size within each mate file from the paired ends. I formerly checked out mrsFast and saw it can't handle this type of data. Has anyone else bumped up against this case that can recommend a tool to get the job done?

With much appreciation,
Roye

Answer 1

[Brian Bushnell]

BBMap works fine with variable-length paired reads. Also, it's been used extensively on huge metagenomic assemblies (up to ~85Gbp in over 200 million contigs), and has no upper limit for total genome size or number of contigs. Lastly... it substantially outperformed masai's sensitivity and accuracy when I directly compared them a while back, though I've not tested yara.