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
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written
by
Roye Rozov
1 answer
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.
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written
by
Brian Bushnell
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