11 months ago by
reformat.sh from BBMap suite.
reformat.sh in1=file_R1.fq.gz in2=file_R2.fq.gz out1=Sampled_R1.fq.gz out2=Sampled_R2.fq.gz parameters_below
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.
Important: srt/sbt flags should not be used with stdin, samplerate, qtrim, minlength, or minavgquality.