Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/seqan/lambda

LAMBDA – the Local Aligner for Massive Biological DatA
https://github.com/seqan/lambda

alignment bioinformatics blast blast-searches high-performance metagenomics ncbi-taxonomy protein-sequences seqan

Last synced: 5 days ago
JSON representation

LAMBDA – the Local Aligner for Massive Biological DatA

Host: GitHub
URL: https://github.com/seqan/lambda
Owner: seqan
License: other
Created: 2015-06-22T09:22:16.000Z (over 9 years ago)
Default Branch: lambda3
Last Pushed: 2024-08-26T11:50:35.000Z (3 months ago)
Last Synced: 2024-11-01T17:02:47.376Z (17 days ago)
Topics: alignment, bioinformatics, blast, blast-searches, high-performance, metagenomics, ncbi-taxonomy, protein-sequences, seqan
Language: C++
Homepage: https://github.com/seqan/lambda
Size: 2.28 MB
Stars: 77
Watchers: 13
Forks: 20
Open Issues: 3
Metadata Files:
- Readme: README.rst
- License: LICENSE-AGPL3.rst

Awesome Lists containing this project

README

Lambda: the Local Aligner for Massive Biological DatA
-----------------------------------------------------

Lambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...

* is highly compatible to BLAST (bit-score and e-value statistics, tab separated and verbose output formats)
* is much faster than BLAST and many other comparable tools
* supports many other input and output formats, including standards-conforming ``.sam`` and ``.bam`` and many compression types
* has special features for species annotation and taxonomic analysis
* is well-documented and easy to use (e.g. provides progress-bars and memory usage estimates)

downloads and installation
--------------------------

usage instructions
------------------

Before you can search, you need to have an index. You can

1. download and unzip a pre-built index from the `wiki `__; or
2. index one yourself (this can take some time but only has to be done once):

% bin/lambda3 mkindexp -d db.fasta

*(in case you want to create a nucleotide index, instead use* ``mkindexn`` *)*

After that running Lambda is as simple as

% bin/lambda3 searchp -q query.fasta -i db.fasta.lba

*(in case you want to perform a nucleotide search, instead use* ``searchn`` *)*

For a list of options, see the help pages:

% bin/lambda3 --help
% bin/lambda3 COMMAND --help

Advanced options are available via ``--full-help`` or the man pages, and more documentation is available
in the `wiki `__.

authorship and copyright
------------------------

Lambda is developed by `Hannes Hauswedell `__ and `Sara Hetzel `__ .

+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| **Please always cite the publication, also if using Lambda in comparisons and pipelines** |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.book.hardcover.open.png | *Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences*; |
| :alt: Please cite | Hannes Hauswedell, Sara Hetzel et al.; |
| :target: https://academic.oup.com/bioinformatics/article/40/3/btae097/7629128 | `Bioinformatics 2024 40 (3) `__; |
| :width: 76px | doi: 10.1093/bioinformatics/btae097 |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| **The original Lambda publication (versions before 3)** |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.book.hardcover.open.png | *Lambda: the local aligner for massive biological data*; |
| :alt: Please cite | Hannes Hauswedell, Jochen Singer, Knut Reinert; |
| :target: http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract | `Bioinformatics 2014 30 (17): i349-i355 `__; |
| :width: 76px | doi: 10.1093/bioinformatics/btu439 |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| **Please respect the license of the software** |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/copyleft.png | Lambda is Free and open source software, so you can use it for any purpose, free of charge. |
| :alt: Respect the license | However certain conditions apply when you (re-)distribute and/or modify Lambda, please respect the |
| :target: https://github.com/seqan/lambda/blob/master/LICENSE.rst | `license `__. |
| :width: 76px | |
+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+

feedback & updates
------------------

+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+
| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.social.github.octocat.png | You can ask questions and report bugs on the `github tracker `__ . |
| :alt: GitHub | Please also `subscribe `__ and/or star us! |
| :target: https://github.com/seqan/lambda/issues | |
| :width: 76px | |
+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+

*icons on this page by Austin Andrews / https://github.com/Templarian/WindowsIcons*