Hi,
I'm using Newbler de novo assembler from the command line (runAssembly), with a set of 18,000 reads.
I'd like to tweak the "repeat" threshold since Newbler estimate that >98% of the reads are repeats, and I end up with 0 contigs...
Here is the command:
runAssembly -ss 12 -sl 16 -sc 1 -ml 25 -mi 80 -o ./newbler seqs.fa
BTW, do somebody have information about how this "repeat detection" step work? I couldn't find much about that in the GS manual... (the manual mention a -rst repeat score threshold, but only for assembly to a reference, with runMapping command)
Thanks,
Laurent
I'm using Newbler de novo assembler from the command line (runAssembly), with a set of 18,000 reads.
I'd like to tweak the "repeat" threshold since Newbler estimate that >98% of the reads are repeats, and I end up with 0 contigs...
Here is the command:
runAssembly -ss 12 -sl 16 -sc 1 -ml 25 -mi 80 -o ./newbler seqs.fa
BTW, do somebody have information about how this "repeat detection" step work? I couldn't find much about that in the GS manual... (the manual mention a -rst repeat score threshold, but only for assembly to a reference, with runMapping command)
Thanks,
Laurent
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