{"id":20153564,"url":"https://github.com/seqan/lambda","last_synced_at":"2025-02-28T06:03:47.337Z","repository":{"id":37588162,"uuid":"37846853","full_name":"seqan/lambda","owner":"seqan","description":"LAMBDA – the Local Aligner for Massive Biological DatA ","archived":false,"fork":false,"pushed_at":"2024-08-26T11:50:35.000Z","size":2392,"stargazers_count":77,"open_issues_count":3,"forks_count":20,"subscribers_count":13,"default_branch":"lambda3","last_synced_at":"2024-11-01T17:02:47.376Z","etag":null,"topics":["alignment","bioinformatics","blast","blast-searches","high-performance","metagenomics","ncbi-taxonomy","protein-sequences","seqan"],"latest_commit_sha":null,"homepage":"https://github.com/seqan/lambda","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/seqan.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-AGPL3.rst","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-06-22T09:22:16.000Z","updated_at":"2024-08-26T11:45:53.000Z","dependencies_parsed_at":"2023-02-13T22:45:56.638Z","dependency_job_id":"5938acaa-66fd-4da0-94c0-30e75e8d2197","html_url":"https://github.com/seqan/lambda","commit_stats":null,"previous_names":[],"tags_count":19,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Flambda","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Flambda/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Flambda/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Flambda/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/lambda/tar.gz/refs/heads/lambda3","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241104116,"owners_count":19910377,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alignment","bioinformatics","blast","blast-searches","high-performance","metagenomics","ncbi-taxonomy","protein-sequences","seqan"],"created_at":"2024-11-13T23:19:44.566Z","updated_at":"2025-02-28T06:03:47.308Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"Lambda: the Local Aligner for Massive Biological DatA\n-----------------------------------------------------\n\nLambda is a versatile local aligner that can perform protein, nucleotide and bisulfite searches. It...\n\n* is highly compatible to BLAST (bit-score and e-value statistics, tab separated and verbose output formats)\n* is much faster than BLAST and many other comparable tools\n* supports many other input and output formats, including standards-conforming ``.sam`` and ``.bam`` and many compression types\n* has special features for species annotation and taxonomic analysis\n* is well-documented and easy to use (e.g. provides progress-bars and memory usage estimates)\n\ndownloads and installation\n--------------------------\n\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n|  **Executables**                                                                                                                                                                                                                      |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. 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                                        |\n|    :alt: Download Executables                                                                                    | `releases page \u003chttps://github.com/seqan/lambda/releases\u003e`__.                                                      |\n|    :target: https://github.com/seqan/lambda/releases                                                             |                                                                                                                    |\n|    :width: 76px                                                                                                  |                                                                                                                    |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n|  **Source code**                                                                                                                                                                                                                      |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. 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                             |\n|    :alt: Build from source                                                                                       | specific system (and thus faster). For instructions, please see the                                                |\n|    :target: https://github.com/seqan/lambda/wiki                                                                 | `wiki \u003chttps://github.com/seqan/lambda/wiki\u003e`__.                                                                   |\n|    :width: 76px                                                                                                  |                                                                                                                    |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n\nusage instructions\n------------------\n\n\nBefore you can search, you need to have an index. You can\n\n1. download and unzip a pre-built index from the `wiki \u003chttps://github.com/seqan/lambda/wiki\u003e`__; or\n2. index one yourself (this can take some time but only has to be done once):\n\n::\n\n    % bin/lambda3 mkindexp -d db.fasta\n\n*(in case you want to create a nucleotide index, instead use* ``mkindexn`` *)*\n\nAfter that running Lambda is as simple as\n\n::\n\n    % bin/lambda3 searchp -q query.fasta -i db.fasta.lba\n\n*(in case you want to perform a nucleotide search, instead use* ``searchn`` *)*\n\nFor a list of options, see the help pages:\n\n::\n\n    % bin/lambda3 --help\n    % bin/lambda3 COMMAND --help\n\nAdvanced options are available via ``--full-help`` or the man pages, and more documentation is available\nin the `wiki \u003chttps://github.com/seqan/lambda/wiki\u003e`__.\n\nauthorship and copyright\n------------------------\n\nLambda is developed by `Hannes Hauswedell \u003cmailto:h2 (æð) fsfe.org\u003e`__ and `Sara Hetzel \u003cmailto:hetzel (æð) molgen.mpg.de\u003e`__ .\n\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n|  **Please always cite the publication, also if using Lambda in comparisons and pipelines**                                                                                                                                            |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. 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*;                             |\n|    :alt: Please cite                                                                                             | Hannes Hauswedell, Sara Hetzel et al.;                                                                             |\n|    :target: https://academic.oup.com/bioinformatics/article/40/3/btae097/7629128                                 | `Bioinformatics 2024 40 (3) \u003chttps://academic.oup.com/bioinformatics/article/40/3/btae097/7629128\u003e`__;             |    \n|    :width: 76px                                                                                                  | doi: 10.1093/bioinformatics/btae097                                                                                |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n|  **The original Lambda publication (versions before 3)**                                                                                                                                                                              |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. image:: https://raw.githubusercontent.com/seqan/lambda/gh-pages/images_readme/appbar.book.hardcover.open.png  | *Lambda: the local aligner for massive biological data*;                                                           |\n|    :alt: Please cite                                                                                             | Hannes Hauswedell, Jochen Singer, Knut Reinert;                                                                    |\n|    :target: http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract                                 | `Bioinformatics 2014 30 (17): i349-i355 \u003chttp://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract\u003e`__; |\n|    :width: 76px                                                                                                  | doi: 10.1093/bioinformatics/btu439                                                                                 |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| **Please respect the license of the software**                                                                                                                                                                                        |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. 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.                        |\n|    :alt: Respect the license                                                                                     | However certain conditions apply when you (re-)distribute and/or modify Lambda, please respect the                 |\n|    :target: https://github.com/seqan/lambda/blob/master/LICENSE.rst                                              | `license \u003chttps://github.com/seqan/lambda/blob/master/LICENSE.rst\u003e`__.                                             |\n|    :width: 76px                                                                                                  |                                                                                                                    |\n+------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n\nfeedback \u0026 updates\n------------------\n\n+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n| .. 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 \u003chttps://github.com/seqan/lambda/issues\u003e`__ .         |\n|    :alt: GitHub                                                                                                   | Please also `subscribe \u003chttps://github.com/seqan/lambda/subscription\u003e`__ and/or star us!                           |\n|    :target: https://github.com/seqan/lambda/issues                                                                |                                                                                                                    |\n|    :width: 76px                                                                                                   |                                                                                                                    |\n+-------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------+\n\n*icons on this page by Austin Andrews / https://github.com/Templarian/WindowsIcons*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Flambda","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Flambda","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Flambda/lists"}