NAME

       fix-trinity-output - Fix output fastq files from Trinity

DESCRIPTION

       Trinity outputs fastq files that have been 'corrected'

       Unfortunately  these  files  are  no longer properly paired and therefore can't be used in
       most aligners such as bowtie2 and snap

       This script attempts to fix that and produce 2 properly paired fastq  files  and  a  fastq
       file containing single reads

OPTIONS

       --left, -l <s>:
              fastq file of left reads

       --right, -r <s>:
              fastq file of right reads

       --output, -o <s>:
              output prefix

       --help, -h:
              Show this message