{"id":13704078,"url":"https://github.com/TimoLassmann/samstat","last_synced_at":"2025-05-05T09:33:03.253Z","repository":{"id":39060182,"uuid":"113824897","full_name":"TimoLassmann/samstat","owner":"TimoLassmann","description":"SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.","archived":false,"fork":false,"pushed_at":"2023-08-03T07:35:17.000Z","size":6997,"stargazers_count":23,"open_issues_count":4,"forks_count":6,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-08-03T21:04:34.331Z","etag":null,"topics":["bioinformatics","next-generation-sequencing","quality-control"],"latest_commit_sha":null,"homepage":"","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/TimoLassmann.png","metadata":{"files":{"readme":"Readme.org","changelog":"ChangeLog","contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-12-11T07:07:01.000Z","updated_at":"2024-04-12T03:15:08.000Z","dependencies_parsed_at":"2023-02-12T20:45:14.012Z","dependency_job_id":"b592a285-716c-42a9-b337-bdaf4b83361f","html_url":"https://github.com/TimoLassmann/samstat","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TimoLassmann%2Fsamstat","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TimoLassmann%2Fsamstat/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TimoLassmann%2Fsamstat/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/TimoLassmann%2Fsamstat/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/TimoLassmann","download_url":"https://codeload.github.com/TimoLassmann/samstat/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224439724,"owners_count":17311511,"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":["bioinformatics","next-generation-sequencing","quality-control"],"created_at":"2024-08-02T21:01:03.891Z","updated_at":"2024-11-13T11:30:47.448Z","avatar_url":"https://github.com/TimoLassmann.png","language":"C","funding_links":[],"categories":["Next Generation Sequencing"],"sub_categories":["BAM File Utilities"],"readme":"[[https://github.com/TimoLassmann/samstat/actions/workflows/cmake.yml][https://github.com/TimoLassmann/samstat/actions/workflows/cmake.yml/badge.svg]]\n* SAMStat\n\nSAMStat is an efficient C program to quickly display statistics of large\nsequence files from next generation sequencing projects. When applied to SAM/BAM\nfiles all statistics are reported for unmapped, poorly and accurately mapped\nreads separately. This allows for identification of a variety of problems, such\nas remaining linker and adaptor sequences, causing poor mapping. Apart from this\nSAMStat can be used to verify individual processing steps in large analysis\npipelines.\n\nSAMStat reports length distribution, base quality distribution, mapping\nstatistics, mismatch, insertion and deletion error profiles. The output is a\nsingle html page:\n\n[[Image of example output][https://user-images.githubusercontent.com/8110320/175869206-6edcb06d-1afc-42f6-bbb8-16a2a18146f0.png]]\n\n* How to install\n\n*SAMstat* depends on the hdf5 library. To install on linux:\n\nUbuntu/Debian:\n\n#+begin_src bash :eval never\nsudo apt-get install -y libhdf5-dev\n#+end_src\n\nOn a mac via [[https://brew.sh][brew]]:\n\n#+begin_src bash :eval never\nbrew install hdf5\n#+end_src\n\nTo build *SAMstat*: \n\n#+begin_src bash :eval never \ngit clone https://github.com/TimoLassmann/samstat.git\ncd samstat\nmkdir build\ncd build\ncmake ..\nmake\nmake install \n#+end_src\n\n* Usage\n\n#+begin_src bash :eval never \nsamstat \u003cfile.sam\u003e  \u003cfile.bam\u003e  \u003cfile.fa\u003e  \u003cfile.fq\u003e ...  \u003coptions\u003e \n#+end_src\n\nFor each input file SAMStat will create a single html page named after the input file name plus a dot =samstat.html= suffix.\n\nAvailable options:\n\n#+begin_src bash :eval never \n   -d/-dir            : Output directory. []\n                        NOTE: by default SAMStat will place reports in the same directory as the input files. \n   -p/-peek           : Report stats only on the first \u003cn\u003e sequences. [unlimited]\n   -t                 : Number of threads. [4]\n                        will only be used when multiple input files are present. \n   --plotend          : Add base and quality plots relative to the read ends. []\n   --seed             : Random number seed. [0]\n   --verbose          : Enables verbose output. []\n\n   -h/-help           : Prints help message. []\n   -v/-version        : Prints version information. []\n#+end_src\n\n\n\n\n* Please cite:\nTimo Lassmann (2023) \"SAMStat 2: quality control for next generation sequencing data.\" Bioinformatics. (2023): btad019, https://doi.org/10.1093/bioinformatics/btad019\n\nLassmann et al. (2010) \"SAMStat: monitoring biases in next generation sequencing data.\" Bioinformatics 27.1 (2011): 130-131. [[https://doi.org/10.1093%2Fbioinformatics%2Fbtq614][doi:10.1093/bioinformatics/btq614]]\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FTimoLassmann%2Fsamstat","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FTimoLassmann%2Fsamstat","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FTimoLassmann%2Fsamstat/lists"}