{"id":18448417,"url":"https://github.com/nextomics/inscan","last_synced_at":"2025-04-15T11:22:29.755Z","repository":{"id":140454429,"uuid":"136862218","full_name":"Nextomics/inScan","owner":"Nextomics","description":"Region based insertion detection from long reads","archived":false,"fork":false,"pushed_at":"2018-06-21T02:16:03.000Z","size":30,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-02-16T13:27:45.185Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Nextomics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-06-11T02:02:48.000Z","updated_at":"2019-12-15T03:42:22.000Z","dependencies_parsed_at":"2023-07-20T22:02:53.026Z","dependency_job_id":null,"html_url":"https://github.com/Nextomics/inScan","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/Nextomics%2FinScan","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FinScan/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FinScan/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Nextomics%2FinScan/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Nextomics","download_url":"https://codeload.github.com/Nextomics/inScan/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249058649,"owners_count":21205976,"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":"2024-11-06T07:15:50.081Z","updated_at":"2025-04-15T11:22:29.738Z","avatar_url":"https://github.com/Nextomics.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# inScan\n\ninScan is devoloping for finding genomic insertion variation from long \nreads(from both Pacbio and Nanopore sequencing).\ninScan differs from the published state of art Structure Variation detecting \ntools(Sniffles and NanoSV) for long reads sequencing technology in two ways. First, \ninScan can find complex insertions when the insert sequence mapped to another \nchromosome. Second, inScan detects insertions in a given region, therefore useful \nfor quickly checking if there are insertions in the region(Short Tandem Repeat region\nfor example) of interest.\n\n# Dependency\n\nPython3.6.2 or later\n\n* pysam\n\n# Getting started\n\n```sh\ngit clone git@github.com:Nextomics/inScan.git\ncd inScan\npython3 inScan.py input.bam input.bed output.json\n```\n\ninScan takes three positional arguments, a bam file, a bed file, a output file name.\n\ninScan has been tested using NGMLR, BWA mem, Minimap2 output bam files. \nGenerally, inScan will work for a bam file with \"SA\" tag.\n\nbed file contains the regions to be tested.\n\noutput json: {\"region\":{\"reads\":[[\"chromosome\",\"start\",\"end\",\"insert_size\"],...],...},...}\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Finscan","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextomics%2Finscan","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextomics%2Finscan/lists"}