Question: all-mapper for differently trimmed mates
gravatar for Roye Rozov
4.1 years ago by
Roye Rozov90
Roye Rozov90 wrote:

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

ADD COMMENTlink modified 4.1 years ago by Brian Bushnell16k • written 4.1 years ago by Roye Rozov90
gravatar for Brian Bushnell
4.1 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Brian Bushnell16k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1293 users visited in the last hour