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jrherr/gist:2c5fed226a1a63f5643a

Created February 8, 2015 16:55
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Rename SPAdes output fasta headers line for pipeline
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gistfile1.txt
sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.name}\1 \2/g" $input > $output
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jrherr commented Feb 8, 2015

The fasta headers from SPAdes output look like this:

>NODE_100_length_628_cov_0.818363_ID_199

I am assuming NODE is the de Bruijn graph node, length is the contig length, coverage is the percent read coverage for the contig, and ID is (I guess) an arbitrary ID from SPAdes.

See here: http://bit.ly/1xQcAzm

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