Question: Simultaneous multiple read recruitment with BBMap?
0
gravatar for Rebecs Garner
2.1 years ago by
Canada/Montreal/Concordia University
Rebecs Garner0 wrote:

Hey there,

I have a co-assembly (assembled from 3 sets of PE reads) and would like to recruit all 3 read sets to the co-assembly at the same time. Is this type of mapping possible with BBMap? If so, how do you format the bbmap command?

Many thanks in advance!

Rebecca

mapping bbmap • 825 views
ADD COMMENTlink written 2.1 years ago by Rebecs Garner0

What do you mean by

would like to recruit all 3 read sets to the co-assembly at the same time

Are you referring to aligning your reads to an assembly made from these 3 sets of reads? While BBMap has some programs (e.g. tadpole.sh) that can do k-mer based assembly it is mainly an alignment program. You could simply cat the three sets of files together and align against the reference.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by GenoMax96k

Hello,

Exactly, the co-assembly was assembled from a combination of these 3 read sets. What I'm looking to do is align the 3 read sets to the co-assembled contigs - I was hoping there'd be an option in BBMap for handling multiple read sets. But if there isn't, I think your solution of using cat could work, I'll check it out, thanks!

ADD REPLYlink written 2.1 years ago by Rebecs Garner0
1
gravatar for GenoMax
2.1 years ago by
GenoMax96k
United States
GenoMax96k wrote:

You could use bbwrap.sh if you don't want to cat the inputs.

$ bbwrap.sh

Last modified April 21, 2015

Description:  Wrapper for BBMap to allow multiple input and output files for the same reference.

To index:                 bbwrap.sh ref=<reference fasta>
To map:                   bbwrap.sh in=<file,file,...> out=<file,file,...>
To map without an index:  bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
To map pairs and singletons and output them into the same file:
bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append

Other Parameters:

in=<file,file>    Input sequences to map.
mapper=bbmap      Select mapper.  May be BBMap, BBMapPacBio, 
                  or BBMapPacBioSkimmer.
append=f          Append to files rather than overwriting them.  
                  If append is enabled, and there is exactly one output file,
                  all output will be written to that file.
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by GenoMax96k

I think this might be exactly the answer I was looking for - thank you so much! I did test out cat though and it yielded the expected results. Thank you so kindly for your help!

ADD REPLYlink written 2.1 years ago by Rebecs Garner0
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