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Update README.md
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sfchen authored Jul 4, 2018
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-I, --in2 read2 input file name (string [=])
-O, --out2 read2 output file name (string [=])
-6, --phred64 indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
-z, --compression compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
-z, --compression compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4. (int [=4])
--stdout output passing-filters reads to STDOUT. This option will result in interleaved FASTQ output for paired-end input. Disabled by defaut.
--interleaved_in indicate that <in1> is an interleaved FASTQ which contains both read1 and read2. Disabled by defaut.
--reads_to_process specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
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-R, --report_title should be quoted with ' or ", default is "fastp report" (string [=fastp report])
# threading options
-w, --thread worker thread number, default is 3 (int [=3])
-w, --thread worker thread number, default is 2 (int [=2])
# output splitting options
-s, --split split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
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