Microbial 'omics

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anvi-script-gen-pseudo-paired-reads-from-fastq [program]

A script that takes a FASTQ file that is not paired-end (i.e., R1 alone) and converts it into two FASTQ files that are paired-end (i.e., R1 and R2). This is a quick-and-dirty workaround that halves each read from the original FASTQ and puts one half in the FASTQ file for R1 and puts the reverse-complement of the second half in the FASTQ file for R2. If you've ended up here, things have clearly not gone very well for you, and Evan, who battled similar battles and ended up implementing this solution wholeheartedly sympathizes.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Can provide


Can consume



This program takes in a short-reads-fasta file and tries to recreate what paired reads for the data in that fasta file might look like.

An arbitrarily chosen half of the reads will be put into the R1 output, while the other half will be reverse complemented and put into the R2 output.

For example, if you ran

anvi-script-gen-pseudo-paired-reads-from-fastq -f short-reads-fasta \ -O MY_READS

Then you would end up with two files:

  • MY_READS_1.fastq which contains half of the reads straight out of your input file
  • MY_READS_2.fastq which contains the reverse complement of the other half of the reads.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.