{"id":18046620,"url":"https://github.com/ltla/cruktools","last_synced_at":"2025-04-05T04:24:49.377Z","repository":{"id":82716749,"uuid":"106588277","full_name":"LTLA/CRUKtools","owner":"LTLA","description":" Assorted scripts for running server jobs at CRUK CI","archived":false,"fork":false,"pushed_at":"2019-01-19T13:35:58.000Z","size":21,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-10T12:29:11.177Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LTLA.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2017-10-11T17:43:12.000Z","updated_at":"2021-03-10T16:03:30.000Z","dependencies_parsed_at":null,"dependency_job_id":"57909e35-2348-498a-8cd3-886264b6dd12","html_url":"https://github.com/LTLA/CRUKtools","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FCRUKtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FCRUKtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FCRUKtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LTLA%2FCRUKtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LTLA","download_url":"https://codeload.github.com/LTLA/CRUKtools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247288092,"owners_count":20914298,"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":"2024-10-30T19:08:13.369Z","updated_at":"2025-04-05T04:24:49.354Z","avatar_url":"https://github.com/LTLA.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CRUK tools\n\nThis repository provides some tools for processing genomics data on the CRUK Cambridge Institute SLURM server.\n\n**Alignment**\n\n- `solo_align.sh` provides a script for aligning a single library (single-end or paired-end).\n- `multi_align.sh` is a convenience wrapper to submit alignment jobs for many libraries in a data set.\n- `guess_encoding.py` guesses the Phred encoding for the aligner.\n\nAlignment is performed using the [_subread_](http://subread.sourceforge.net/) aligner.\nIt also requires [_samtools_](http://www.htslib.org/) and [_MarkDuplicates_](https://broadinstitute.github.io/picard/).\n\n**Read counting**\n\n`counter.R` provides a template for read counting to produce a gene-by-sample count matrix.\nIt requires specification of the BAM files for which to perform the counting as well as a set of GTF annotation files.\nIt will use the `featureCounts` function in the [_Rsubread_](https://bioconductor.org/packages/Rsubread) package.\n\n**Data mangling**\n\n- `cram2fastq.sh` will convert a CRAM file into FASTQ for entry into the alignment pipelines above.\n- `sanger_dump.sh` will convert an entire folder of CRAM files into FASTQs.\n\n**Other**\n\n`cell_ranger.sh` will call the [_CellRanger_](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) pipeline to create a count matrix for single-cell transcriptomics data from the 10X Genomics platform.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fcruktools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fltla%2Fcruktools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fltla%2Fcruktools/lists"}