AlienTrimmer Question

[cement_head]

Hello,

When using AlienTrimmer to trim PE data, it generates three files: R1 trimmed, R2 trimmed, and a "singles" file (one read failed the QC test). When you do a de novo assembly, does one use all three files? Or just the R1 / R2 PE files?

Thanks,
Andor

[Brian Bushnell]

Some assemblers can take both paired and unpaired reads at the same time, but if you have sufficient coverage with the paired reads only, I'd recommend throwing away the singletons. They add complexity and are likely to be lower quality anyway; for example, they may be reads that should have been removed (due to the presence of adapters or other non-genomic artifacts) but were not removed because they had so many errors it prevented detection.

[cement_head]

Some assemblers can take both paired and unpaired reads at the same time, but if you have sufficient coverage with the paired reads only, I'd recommend throwing away the singletons. They add complexity and are likely to be lower quality anyway; for example, they may be reads that should have been removed (due to the presence of adapters or other non-genomic artifacts) but were not removed because they had so many errors it prevented detection.

Cheers - thanks - that was exactly the direction I was leaning.