Oh, sorry, the command I gave you was for interleaved reads, so those are all false positive merges. For pairs in separate files, the command would be:
bbmerge.sh in1=R1.fq in2=R2.fastq ihist=ihist.txt reads=100000
As for whether you merge the reads before assembly, that depends on the assembler. AllPathsLG does its own merging; Ray seems to do well with merged reads; SoapDenovo creates worse assemblies with merged reads; there's no single rule. I've never used Geneious, so I don't know if it would help. As with many options, such as trimming and subsampling, sometimes the only way to get the best assembly is to try both ways.
If you do merge the reads, I suggest using the default settings:
bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq outu1=unmerged1.fq outu2=unmerged2.fq
...then feed the assembler both the merged and unmerged reads. Many or most assemblers will accept both paired and unpaired reads; merging should not be done for assemblers that don't allow you to feed them both paired and unpaired reads simultaneously, as low-complexity genomic regions will not merge as well.
bbmerge.sh in1=R1.fq in2=R2.fastq ihist=ihist.txt reads=100000
As for whether you merge the reads before assembly, that depends on the assembler. AllPathsLG does its own merging; Ray seems to do well with merged reads; SoapDenovo creates worse assemblies with merged reads; there's no single rule. I've never used Geneious, so I don't know if it would help. As with many options, such as trimming and subsampling, sometimes the only way to get the best assembly is to try both ways.
If you do merge the reads, I suggest using the default settings:
bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq outu1=unmerged1.fq outu2=unmerged2.fq
...then feed the assembler both the merged and unmerged reads. Many or most assemblers will accept both paired and unpaired reads; merging should not be done for assemblers that don't allow you to feed them both paired and unpaired reads simultaneously, as low-complexity genomic regions will not merge as well.
Comment