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Old 08-14-2017, 09:58 AM   #161
Brian Bushnell
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Quote:
Originally Posted by SNPsaurus View Post
I take a subset from each file and then cat the subsets together. That would be faster than combining the inputs with cat, at least.
True, this works well. Alternatively, for interleaved files, you can do this:

Code:
cat a.fq b.fq c.fq | reformat.sh in=stdin.fq out=sampled.fq interleaved samplerate=0.1
...which avoids writing temp files. Won't work for twin paired files, though, unless you do something tricky with named pipes.

To avoid wasting disk space and bandwidth, I normally keep all fastq files gzipped at all times. Using pigz for parallel compression, or compression level 2 (zl=2 flag), will eliminate much of the speed penalty from dealing with compressed files; and if you are I/O limited, compressed files tend to speed things up.

I don't have any plans at present to add multiple input file support (or wildcard support) to Reformat, but I'll put it on my list and consider it. It's something I've occasionally wanted also.
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Old 09-11-2017, 02:21 PM   #162
TomHarrop
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Default Can BBmap remove reads containing homopolymers?

Hi BBmap-ers,

Say I want to remove reads with more than 5 consecutive identical nucleotides. Is there a homopolymer/ polyX filtering option with BBDuk or reformat.sh?

Thanks!

Tom
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Old 09-11-2017, 02:24 PM   #163
Brian Bushnell
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There is no homopolymer filter, per se, but you can accomplish that like this:

Quote:
bbduk.sh in=reads.fq out=clean.fq literal=AAAAAA,CCCCCC,GGGGGG,TTTTTT k=6 mm=f
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Old 09-11-2017, 02:35 PM   #164
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Great, thanks!
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