Simultaneous multiple read recruitment with BBMap?

Question

[Rebecs Garner]

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

[GenoMax]

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.

[Rebecs Garner]

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!

Answer 1

[GenoMax]

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.

[Rebecs Garner]

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!