{"id":25596872,"url":"https://github.com/nanoporetech/spliced_bam2gff","last_synced_at":"2025-04-13T02:33:17.438Z","repository":{"id":48249418,"uuid":"316323589","full_name":"nanoporetech/spliced_bam2gff","owner":"nanoporetech","description":null,"archived":false,"fork":false,"pushed_at":"2021-08-04T10:21:19.000Z","size":16728,"stargazers_count":5,"open_issues_count":3,"forks_count":2,"subscribers_count":16,"default_branch":"master","last_synced_at":"2025-04-06T08:02:15.834Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Go","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/nanoporetech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-11-26T19:46:20.000Z","updated_at":"2024-08-19T08:18:50.000Z","dependencies_parsed_at":"2022-07-29T18:39:48.535Z","dependency_job_id":null,"html_url":"https://github.com/nanoporetech/spliced_bam2gff","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fspliced_bam2gff","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fspliced_bam2gff/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fspliced_bam2gff/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fspliced_bam2gff/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanoporetech","download_url":"https://codeload.github.com/nanoporetech/spliced_bam2gff/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248657796,"owners_count":21140842,"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":[],"created_at":"2025-02-21T12:34:59.855Z","updated_at":"2025-04-13T02:33:17.415Z","avatar_url":"https://github.com/nanoporetech.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"![ONT_logo](/ONT_logo.png)\n-----------------------------\n\nspliced_bam2gff - a tool to convert spliced BAM alignments into GFF2 format\n===========================================================================\n[![bioconda-badge](https://anaconda.org/bioconda/spliced_bam2gff/badges/installer/conda.svg)](https://anaconda.org/bioconda/spliced_bam2gff)\n\nThe **spliced_bam2gff** tool converts [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) alignments, produced by spliced aligners (such as [minimap2](https://github.com/lh3/minimap2), [gmap](http://research-pub.gene.com/gmap)), into a [GFF2](https://www.ensembl.org/info/website/upload/gff.html) format.\n\nBy default, introns are created based on the `N` cigar feature. Alternatively, if `-d` (i.e. for deletion) is specified, any deletions larger than the limit will be classified as an intron.\nThe orientation of the GFF2 features is determined by the `XS` strand tag and SAM flags depending on the aligner.\n\nThe tool supports splitting the output into *loci* and *bundles of loci* with a minimum number of features, which enables easy parallelisation of downstream analyses.\nThe generated GFF2 files can be compared to a reference annotation using the [gffcompare](https://github.com/gpertea/gffcompare) tool.\n\n## Installation\n\nThe best way to install the tool is from bioconda:\n\n- Make sure you have [miniconda3](https://docs.conda.io/en/latest/miniconda.html) installed.\n- Set up the bioconda channel according to the [instructions](://bioconda.github.io/user/install.html).\n- Install the tool by issuing `conda install spliced_bam2gff`\n\n## Usage\n\n```\nUsage of ./spliced_bam2gff:\n  -L string\n        Write output partitioned into \"loci\" to this directory. Turns of output to stdout.\n  -M    Input is from minimap2.\n  -S    Do NOT discard secondary and supplementary alignments.\n  -V    Print out version.\n  -b int\n        Bundle together loci in batches with at least this size. (default -1)\n  -d int\n        Classify all deletions larger than this as introns (-1 means off). (default -1)\n  -g    Use strand tag as feature orientation then read strand if not available.\n  -h    Print out help message.\n  -s    Use read strand (from BAM flag) as feature orientation.\n  -t int\n        Number of cores to use. (default 8)\n```\n\nExamples\n========\n\n### Convert alignments generated by `minmap2 -x splice`\n\n```\nspliced_bam2gff -M ./test_data/sirv_simulated.bam \u003e ./test_data/sirv_simulated_mm2.gff\n```\n\nConvert while classifying all deletions larger than 20 as introns:\n```\nspliced_bam2gff -d 20 -M ./test_data/sirv_simulated.bam \u003e ./test_data/sirv_simulated_mm2.gff\n```\n\nConvert to GFF2 and split the output into loci separated by regions with no coverage:\n```\nspliced_bam2gff -M -L ./test_data/sirv_simulated_mm2_loci -s ./test_data/sirv_simulated.bam\n```\n\nConvert to GFF2 and split the output into bundles of loci with at least two thousand features:\n```\nspliced_bam2gff -b 2000 -M -L ./test_data/sirv_simulated_mm2_loci -s ./test_data/sirv_simulated.bam\n```\n\n### Convert alignments generated by `gmap`\n\n```\nspliced_bam2gff  -g ./test_data/sirv_errors_gmap.bam \u003e ./test_data/test_out_err.gff\n```\n\nRunning tests\n============\n\nFor running tests the following dependencies have to be installed:\n\n- [gffcompare](https://github.com/gpertea/gffcompare)\n\nWhich is easy to install using [bioconda](https://bioconda.github.io). \nLook into the `Makefiles` for targets testing the tools on simulated and real data.\n\nHelp\n====\n\n## Licence and Copyright\n\n(c) 2020 Oxford Nanopore Technologies Ltd.\n\nThis Source Code Form is subject to the terms of the Mozilla Public\nLicense, v. 2.0. If a copy of the MPL was not distributed with this\nfile, You can obtain one at http://mozilla.org/MPL/2.0/.\n\n## FAQs and tips\n\n- The [GFF2](https://www.ensembl.org/info/website/upload/gff.html) files can be visualised using [IGV](http://software.broadinstitute.org/software/igv).\n- The GFF2 files can be converted to GFF3 or GTF using the [gffread](https://bioconda.github.io/recipes/gffread/README.html) utility.\n\n## References and Supporting Information\n\nSee the post announcing the tool at the Oxford Nanopore Technologies community [here](https://community.nanoporetech.com/posts/new-transcriptomics-analys).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fspliced_bam2gff","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanoporetech%2Fspliced_bam2gff","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fspliced_bam2gff/lists"}