BiobaseFasta: streaming FASTA parser

[ bioinformatics, gpl, library ] [ Propose Tags ]

Stream-based handling of FASTA files. The user selects a window size, the library then handles the window. For each window, the previous (past) window is available, in case some data sits on the boundary between windows.

FastaTool is a simple tool providing information on FASTA files, and allowing to extract sequences and subsequences.

Greg Schwartz' package is a lot more complete. This one is mostly tailored to my usage requirements (and may at some point use his library).

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Dependencies base (>=4.7 && <5.0), BiobaseTypes (==0.1.4.*), bytestring, deepseq, lens, resourcet (>=1.0), streaming (>=0.1), streaming-bytestring (>=0.1) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2011-2018
Author Christian Hoener zu Siederdissen, Florian Eggenhofer
Category Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at Wed Dec 12 23:43:51 UTC 2018
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Downloads 2967 total (129 in the last 30 days)
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Status Hackage Matrix CI
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Last success reported on 2018-12-12 [all 1 reports]


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A Haskell library for FASTA-file handling.

The version does streaming using the 'streaming' library.

The library is, in general, in a "preview" state. In cases where you need to scan large FASTA files fast and with low memory overhead, the functions within should already be useable enough.

The wikipedia has information on the format:


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany