Talk:Newbler parameter '-a' (minimum contig length) not working

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11/22/11: Ran Newbler via command line now to see if -a works outside of Galaxy interface:

  • Method
  1. copied Newbler command from Galaxy run, just changed the filenames for local use, deleted _mcf, -vs, -fe and -fi options

runAssembly -o uro-assembled -cpu 6 -rip -e 0 -mi 90 -ml 40 -minlen 20 -info -qo -ss 12 -sl 16 -sc 1 -ais 2 -a 100 -vt ../../trimfileforUrPHO.fas -cdna -ig 500 -it 100 -icc 100 -icl 3 ../UrEy.sff ../PHO_F5BN4WZ03.sff

  • Results from command line run

454Allcontigs.fna has many more contigs (from 3700 with Galaxy's Newbler to 4094). 752/4094 contigs are less than 100 in length, so this -a problem must be a Newbler-wide bug and not due to the wrapper.

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