This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description

Utilities to work with paired sequence files

Copyright 2012 Lance Parsons <>

BSD 2-Clause License - See LICENSE.txt


  1. Install BioPython version 1.57 or above (required for

    pip install BioPython
  2. Install paired_sequence_utils:

    pip install paired_sequence_utils

Takes two sequence files as input and matches up paired sequences, outputting them separately from orphan sequences. Useful when paired reads are in two separate files and were filtered separately. By default, paired reads are output interleaved with another (read 1 and read 2 of a pair, then read 1 and read 2 of a second pair, etc.). If the paired output file is specified twice, the first read is output to the in the first file, the second read of a pair is output in the second file.


Output paired reads interleaved to STDOUT and the single reads to STDERR: read1.fastq read2.fastq > paired_reads.fastq 2>single_reads.fastq

Output paired reads to separate files: read1.fastq read2.fastq -p read1_paired.fastq -p read2_paired.fastq -s single_reads.fastq

NOTE: This script requires BioPython ( version 1.57 or above

Split multiple fastq files by matching barcodes in one of the sequence files. Barcodes in the tab-delimited barcodes.txt file are matched against the beginning of the specified index read By default, barcodes must match exactly, but –mistmatches can be set higher if desired If input files are gzipped, the output is as well. Compression can be forced with the –gzip option.


Split a an Illumina paired-end run where the index read is read 2, the forward read is read 1, and the reverse read is read 3: --bcfile barcodes.txt read1.fastq read2_index.fastq read3.fastq --idxread 2 --suffix .fastq
Release History

Release History


This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

Show More

Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
paired_sequence_utils-0.1.tar.gz (7.4 kB) Copy SHA256 Checksum SHA256 Source May 31, 2012

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting