View Single Post
Old 07-23-2015, 05:35 AM   #2
Location: USA

Join Date: Sep 2014
Posts: 18

Hi Brian,

Thanks again for your time in developing these tools. Could you clarify this statement from a previous post (

For extending paired reads so that they overlap, only “extendright” is needed, so “extendleft” should be set to zero.
Example for error correction and extending 100 nt for PE files:
java -Xmx24g -cp /path/to/bbmap/current assemble.Tadpole in=r1.fastq.gz extend=r1.fastq.gz oute=r1.fastq.gz mode=extend extendleft=0 extendright=100 ecc=t

java -Xmx24g -cp /path/to/bbmap/current assemble.Tadpole in=r2.fastq.gz extend=r2.fastq.gz oute=r2.fastq.gz mode=extend extendleft=0 extendright=100 ecc=t
You still recommending the previois approach or is better to Interleave the pair-end files (r1/r2) and follow the following command?

Code: in=reads.fq out=extended.fq mode=extend el=50 er=50 ecc

Thanks again

Last edited by GenoMax; 07-23-2015 at 06:02 AM. Reason: Fixed CODE tag
vingomez is offline   Reply With Quote