seqan / Lambda

Lambda: the Local Aligner for Massive Biological DatA

Lambda is a local aligner optimized for many query sequences and searches in protein space. It...

• is highly compatible to BLAST (bitscore 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-conformant .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

+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | Executables | +------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.disk.download.png | Pre-built executables for GNU/Linux, Mac and FreeBSD are available from the | | :alt: Download Executables | releases page <https://github.com/seqan/lambda/releases>. | | :target: https://github.com/seqan/lambda/releases | | | :width: 76px | | +------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | Source code | +------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.column.three.png | You can also build lambda from source which will result in binaries optimized for your | | :alt: Build from source | specific system (and thus faster). For instructions, please see the | | :target: https://github.com/seqan/lambda/wiki | wiki <https://github.com/seqan/lambda/wiki>. | | :width: 76px | | +------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+

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 <https://github.com/seqan/lambda/wiki>__; or
2. index one yourself (this can take some time but only has to be done once):

::

% bin/lambda2 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/lambda2 searchp -q query.fasta -i db.fasta.lambda

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

For a list of options, see the help pages:

::

% bin/lambda2 --help
% bin/lambda2 COMMAND --help

Advanced options are available via --full-help or the man pages, and more documentation is available in the wiki <https://github.com/seqan/lambda/wiki>__.

authorship and copyright

Lambda is being developed by Hannes Hauswedell <mailto:[email protected]>, but it incorporates a lot of work from other members of the SeqAn project <http://www.seqan.de>.

+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | 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 | 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 <http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract>; | | :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 <https://github.com/seqan/lambda/blob/master/LICENSE.rst>. | | :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 <https://github.com/seqan/lambda/issues>__ . | | :alt: GitHub | Please also subscribe <https://github.com/seqan/lambda/subscription>__ and/or star us! | | :target: https://github.com/seqan/lambda/issues | | | :width: 76px | | +-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.email.png | To stay up to date via e-mail, please subscribe to the | | :alt: Newsletter | newsletter <https://lists.fu-berlin.de/listinfo/lambda-users>. There is on average less than one e-mail | | :target: https://lists.fu-berlin.de/listinfo/lambda-users | per month. | | :width: 76px | | +-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+ | .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.social.twitter.png | You can also follow SeqAn on twitter <https://twitter.com/SeqAnLib> to receive updates on Lambda. | | :alt: Newsletter | | | :target: https://twitter.com/SeqAnLib | | | :width: 76px | | +-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+

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