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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
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Release History


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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

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