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Repository sailfish

Name: sailfish

Owner: bgruening

Synopsis: Sailfish is a tool for transcript quantification from RNA-seq data

Detailed description:

Sailfish is a tool for transcript quantification from RNA-seq data. It requires a set of target transcripts
(either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference
transcripts and a (set of) fasta/fastq file(s) containing your reads. Sailfish runs in two phases; indexing and quantification.
The indexing step is independent of the reads, and only needs to be run once for a particular set of reference transcripts and
choice of k (the k-mer size). The quantification step, obviously, is specific to the set of RNA-seq reads and is thus run more frequently
Additional covariates may optionally be provided to further inform the peak-calling process.

https://github.com/kingsfordgroup/sailfish

Content homepage: http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Development repository: https://github.com/bgruening/galaxytools/tree/master/tools/sailfish

Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/bgruening/sailfish/1b4ed566a41c

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/sailfish

Type: unrestricted

Revision: 5:1b4ed566a41c

This revision can be installed: True

Times cloned / installed: 1890

Repository README files - may contain important installation or license information

Readme files

Galaxy wrappers for sailfish ===================================== These wrappers are copyright 2014 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. All rights reserved. See the licence text below. Currently tested with sailfish 0.10.1 Automated Installation ====================== Galaxy should be able to automatically install the sailfish for you. History ======= ======== ====================================================================== Version Changes -------- ---------------------------------------------------------------------- v0.6.3.0 - First release -------- ---------------------------------------------------------------------- v0.10.1 - Second release ======== ====================================================================== Bug Reports =========== You can file an issue here https://github.com/bgruening/galaxytools/issues or ask us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.