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Input via ` input cmd'

Dinghua Li edited this page Jun 18, 2015 · 1 revision

WARNING: all reads input via --input-cmd are taken by MEGAHIT as Single-ended.

  • Input from two fasta files sample_1.fa and sample_2.fa:
--input-cmd "cat sample_[12].fa"
  • Input from all gzip'ed fastq files in current directory:
--input-cmd "zcat *.fastq.gz"
  • Assume that fastq-dump is installed, input from a sra file xxx.sra:
--input-cmd "fastq-dump -Z --fasta xxx.sra"
  • Mixed fastq and fasta (supported since v0.2.0):
--input-cmd "cat 1.fa 2.fq"
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