Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

Finds and discards exact duplicate reads in fastq files.

Project description

.. image:: https://travis-ci.org/mvdbeek/dedup_hash.svg?branch=master
:target: https://travis-ci.org/mvdbeek/dedup_hash

dedup_hash
----------------------------


This is a commandline utility to remove exact duplicate reads
from paired-end fastq files. Reads are assumed to be in 2 separate
files. Read sequences are then concatenated and a short hash is calculated on
the concatenated sequence. If the hash has been previsouly seen the read will
be dropped from the output file. This means that reads that have the same
start and end coordinate, but differ in lengths will not be removed (but those
will be "flattened" to at most 1 occurence).

This algorithm is very simple and fast, and saves memory as compared to
reading the whole fastq file into memory, such as fastuniq does.

Installation
------------

depdup_city relies on the cityhash python package,
which supports python-2.7 exclusively.

``pip install dedup_hash``





History
-------

.. to_doc

---------------------
0.1.1 (2016-11-23)
---------------------
* Make python2/3 compatible
* Use smhasher as default hasher and add options for cityhash and hashxx
* Testing enhancements

* Initial version
---------------------
0.1.0 (2016-11-16)
---------------------

* Initial version

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for dedup_hash, version 0.1.1
Filename, size File type Python version Upload date Hashes
Filename, size dedup_hash-0.1.1.tar.gz (4.3 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page