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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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polishment using other tools #202

Closed wangjiawen2013 closed 4 years ago

wangjiawen2013 commented 4 years ago

Hello, Does the quick start (./wtdbg2.pl -t 16 -x rs -g 4.6m -o dbg reads.fa.gz) wraps the following three steps: 1 ./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t 16 -fo dbg 2 ./wtpoa-cns -t 16 -i dbg.ctg.lay.gz -fo dbg.raw.fa 3 minimap2 -t16 -ax map-pb -r2k dbg.raw.fa reads.fa.gz | samtools sort -@4 >dbg.bam samtools view -F0x900 dbg.bam | ./wtpoa-cns -t 16 -d dbg.raw.fa -i - -fo dbg.cns.fa If so, if i wanna polish the data using other tools, does it means that I must run the above three steps separately ? namely, run step 1 and 2 first, then run step3 with other polishment tools ?

ruanjue commented 4 years ago

Yes, you are right. Besides, you can run other polish tool after all those 3 steps finished.