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Update assembly.rst
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nkleinbo committed Sep 24, 2019
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Expand Up @@ -114,7 +114,7 @@ Generate and assemble trimmed reads

The trimming stage identifies unsupported regions in the input and trims or splits reads to their longest supported range. The assembly stage makes a final pass to identify sequencing errors; constructs the best overlap graph (BOG); and outputs contigs, an assembly graph, and summary statistics::

canu -trim-assemble -d ~/workdir/assembly_small -p assembly genomeSize=3M useGrid=false -nanopore-corrected ~/workdir/correct_small/assembly.correctedReads.fasta.gz
canu -trim-assemble -d ~/workdir/assembly_small -p assembly genomeSize=2M useGrid=false -nanopore-corrected ~/workdir/correct_small/assembly.correctedReads.fasta.gz

After that is done, inspect the results. We can get a quick view on the number of generated contigs with::

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