Can anyone recommend a tool to filter my paired end Illumina reads (something like mean Q score), either shuffled together in the same file or in separate files, while maintaining the read order? i.e if 1 read of a pair fails, remove it's mate as well (and preferably stick it in a singlets file or something)? I'm aware of the Galaxy web tool but don't want to upload gigs and gigs of sequence data...
Thanks in advance!
Thanks in advance!
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