Input via ` input cmd' - voutcn/megahit GitHub Wiki

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"