Sampling Fastq reads using resorvior sampling
Ubuntu 18.04
gcc >= 4.8
zlib
Heng Li's kseq.h (included in this repository)
After clone this respository do the following
$ cd fastq-resorvior
$ gcc -O2 -o fastq-resorvior fastq-resorvior.c -lz
./fastq-resorvior -m mode [options] in1.fastq[,in2.fastq] out1.fastq[,out2.fastq]
[options]
-h This help message
-f FLT Factor of sampling. If -k is also set, then the smaller value using
this factor and -k result will be sampled [default=1.0]
-k INT Actual number of reads to sample. If -f is also set, then the smaller
values using -f and -k will be used [default=all_reads]
-m STR Sequencing read mode either s or p to denote single end and paried end
[default=s]
Example command for single end read sampling
./fastq-resorvior in.fastq out.fastq
Example command for paired end read sampling
./fastq-resorvior in1.fastq in2.fastq out1.fastq out2.fastq
Thomas Sunghoon Heo
GPL v3