Question: all-mapper for differently trimmed mates
0
gravatar for Roye Rozov
4.1 years ago by
Roye Rozov90
Israel
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
1
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
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