Originally posted by sirius
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Code:
nesoni samshrimp: output_directory [options] \ reference.fa/.gbk [...] \ [reads: single.fq | single.fa [...]] \ [interleaved: interleaved.fq | interleaved.fa [...]] \ [pairs: left.fq right.fq | left.fa right.fa] \ [shrimp-options: ...options to pass directly to gmapper-ls... ]
If single end, this is the command you want:
nesoni samshrimp: test_out J_mapper.fasta reads: J.fq
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