BiobaseFasta: streaming FASTA parser

[ bioinformatics, gpl, library, program ] [ 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).

[Skip to Readme]
Change log
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
Home page
Bug tracker
Source repo head: git clone git://
Uploaded by ChristianHoener at Wed Dec 12 23:43:51 UTC 2018
Distributions NixOS:
Downloads 2793 total (82 in the last 30 days)
Rating (no votes yet) [estimated by rule of succession]
Your Rating
  • λ
  • λ
  • λ
Status Docs available [build log]
Last success reported on 2018-12-12 [all 1 reports]
Hackage Matrix CI


[Index] [Quick Jump]


Maintainer's Corner

For package maintainers and hackage trustees

Readme for BiobaseFasta-

[back to package description]

Build Status


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