#15 unitigs available before assembly?

[stefanie]

Hello,

I'd like Celera (Cabog) to compute just unitigs for me from Illumina data; at this point I don't need a full assembly. Is there any way to extract a fasta file with the unitigs after the unitigger stage without having to run the entire pipeline all the way to the assembly stage?

Thanks,

Stefanie

[Brian Walenz]

Use stopBefore=cgw to stop after all unitig operations (including splitting), then output unitig sequences from the tigStore with:

tigStore -g gkpStore -t tigStore -d consensus -U

This will output all unitig sequences, including unassembled unitigs that are only a single read.

Alternately, you can finish the assembly with

terminator -o OUTPUT_PREFIX -g gkpStore -t tigStore 5

Which will get you the primary output OUTPUT_PREFIX.asm from which you can generate the posmap files with buildPosMap and asmOutputFasta.

buildPosMap -o OUTPUT_PREFIX -i OUTPUT_PREFIX.asm -g *gkpStore
asmOutputfasta -p OUTPUT_PREFIX < OUTPUT_PREFIX.asm

[stefanie]

great, thank you!