flower: Analyze 454 flowgrams (.SFF files)

[ bioinformatics, program ] [ Propose Tags ]

flower - FLOWgram ExtractoR tools

This is now obsolete, please install the biosff library (which includes the flower exectuable) instead.

The flower executable reads files in SFF-format and produces various output, including sequences with quality, or flowgram data in tabular format. By default, it outputs a textual representation of the data in the SFF-file, much like sffinfo from Roche does.

The flowselect executable extracts reads from SFF-files, generating a new SFF-file with a subset of the reads based on various quality criteria.

The flowt program removes (artificial) duplicates from SFF files. It's currently a work in progress, but included if you'd like to play with it. It's faster than other approaches (e.g. CD-HIT), and ought to be more sensitive and specific, but this needs to be proven.


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Versions [RSS] 0.1, 0.1.1, 0.1.2, 0.2, 0.3, 0.4, 0.5, 0.6, 0.6.1, 0.6.3, 0.6.5, 0.7, 0.7.2
Dependencies array (>=0.1), base (>=3 && <5), binary (>=0.4 && <0.5), bio (>0.4.9), bytestring (>=0.9.1), cmdargs (>=0.5), containers, mtl, random [details]
License LicenseRef-GPL
Author Ketil Malde
Maintainer Ketil Malde <ketil@malde.org>
Category Bioinformatics
Home page http://biohaskell.org/Applications/Flower
Uploaded by KetilMalde at 2013-09-19T06:28:19Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables flowt, flowselect, flower
Downloads 9578 total (35 in the last 30 days)
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Status Docs available [build log]
Successful builds reported [all 1 reports]