Dedupe will merge assemblies, but it will not produce consensus sequences or join overlapping reads; it only removes sequences that are fully contained within other sequences (allowing the specified number of mismatches or edits).
BBMap works pretty well for mapping Nanopore reads, but as GenoMax stated, it has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently. The command I have been using for mapping Nanopore reads:
mapPacBio.sh -Xmx20g k=7 in=reads.fastq ref=reference.fa maxlen=1000 minlen=200 idtag ow int=f qin=33 out=mapped1.sam minratio=0.15 ignorequality slow ordered maxindel1=40 maxindel2=400
The "maxlen" flag shreds them to a max length of 1000; you can set that up to 6000. But I found 1000 gave a higher mapping rate.
BBMap works pretty well for mapping Nanopore reads, but as GenoMax stated, it has a length cap of 6kbp. Reads longer than this will be broken into 6kbp pieces and mapped independently. The command I have been using for mapping Nanopore reads:
mapPacBio.sh -Xmx20g k=7 in=reads.fastq ref=reference.fa maxlen=1000 minlen=200 idtag ow int=f qin=33 out=mapped1.sam minratio=0.15 ignorequality slow ordered maxindel1=40 maxindel2=400
The "maxlen" flag shreds them to a max length of 1000; you can set that up to 6000. But I found 1000 gave a higher mapping rate.
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