Downsampling fastq reads
Hi all,
Do you have recommendations which tool to use to randomly downsample a fastq file to a specified read number? Specifically I am working on shotgun metagenomic data.
Thanks Philipp
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mario_de_manner •
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mario_de_manner •
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rpolicastro
reformat.sh from BBMap suite. Following options are relevant.
reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
skipreads=-1 Skip (discard) this many INPUT reads before processing the rest.
samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
samplereadstarget=0 (srt) Exact number of OUTPUT reads (or pairs) desired.
samplebasestarget=0 (sbt) Exact number of OUTPUT bases desired.
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