Mercurial > repos > mvdbeek > dedup_hash

annotate README.rst @ 0:f33e9e6a6c88 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
author mvdbeek
date Wed, 23 Nov 2016 07:49:05 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
1 .. image:: https://travis-ci.org/mvdbeek/dedup_hash.svg?branch=master
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
2 :target: https://travis-ci.org/mvdbeek/dedup_hash
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
3
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
4 dedup_hash
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
5 ----------------------------
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
6
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
7
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
8 This is a commandline utility to remove exact duplicate reads
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
9 from paired-end fastq files. Reads are assumed to be in 2 separate
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
10 files. Read sequences are then concatenated and a short hash is calculated on
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
11 the concatenated sequence. If the hash has been previsouly seen the read will
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
12 be dropped from the output file. This means that reads that have the same
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
13 start and end coordinate, but differ in lengths will not be removed (but those
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
14 will be "flattened" to at most 1 occurence).
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
15
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
16 This algorithm is very simple and fast, and saves memory as compared to
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
17 reading the whole fastq file into memory, such as fastuniq does.
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
18
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
19 Installation
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
20 ------------
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
21
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
22 depdup_city relies on the cityhash python package,
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
23 which supports python-2.7 exclusively.
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
24
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
25 ``pip install dedup_hash``
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
parents:
diff changeset
26