{"id":26837029,"url":"https://github.com/ibchgenomic/panscape","last_synced_at":"2025-04-30T13:51:31.392Z","repository":{"id":277112119,"uuid":"931149605","full_name":"IBCHgenomic/panscape","owner":"IBCHgenomic","description":"reads to genome, pangenome graphs, summarize and analyze","archived":false,"fork":false,"pushed_at":"2025-02-26T13:07:04.000Z","size":1114,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-30T16:43:55.864Z","etag":null,"topics":["bioinformatics","nanopore-reads","nanopore-sequencing","pacbio-data","pacbio-sequencing"],"latest_commit_sha":null,"homepage":"","language":"Rust","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/IBCHgenomic.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-02-11T19:49:23.000Z","updated_at":"2025-02-26T13:07:08.000Z","dependencies_parsed_at":"2025-03-11T23:25:41.297Z","dependency_job_id":null,"html_url":"https://github.com/IBCHgenomic/panscape","commit_stats":null,"previous_names":["sciencegenome/nanopore-pacbio-all","sciencegenome/panscape","ibchgenomic/panscape"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpanscape","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpanscape/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpanscape/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/IBCHgenomic%2Fpanscape/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/IBCHgenomic","download_url":"https://codeload.github.com/IBCHgenomic/panscape/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251714932,"owners_count":21631806,"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","nanopore-reads","nanopore-sequencing","pacbio-data","pacbio-sequencing"],"created_at":"2025-03-30T16:33:56.537Z","updated_at":"2025-04-30T13:51:31.344Z","avatar_url":"https://github.com/IBCHgenomic.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# panscape\n - from reads to alignments to pangenome, metagenome inclduing the genome annotation using the nanopore and pacbio under one rust binary\n - this will also creates the pangenome database and also the pangenome reads database for rest api. \n - added the support for the pangenome bed files and also the creation of the ancestral states from the bedfiles of the pangenomes. \n - this code will be updated regularly. \n\n ```\n cargo build\n ```\n\n ```\n gauravsablok@genome panscape main ? ./target/debug/panscape -h\n panscape: analyzing pangenomes from reads to stats\n\n Usage: panscape \u003cCOMMAND\u003e\n\n Commands:\n  fasta-convert             convert into fasta\n  clipper-align             clipping the regions from the fastq\n  scanner                   scans the reads for the motifs single occurence\n  motifcatcher              motif plus upstream and the downstream\n  selectedreads             selected reads writer\n  filterreads               filter the reads prior to the length\n  clip-seq                  remove the clip regions from the reads\n  multi-clip-seq            remove the multitags for the fastqfile\n  pangenome                 assemble pangenome\n  minimap                   annotate reads\n  stat                      annotated stats for your file\n  pangenome-summarize       pangenome pre-computed alignment\n  read-multisearch          multisearch reads across the reads\n  paf-annotate              annotate your pangenome paf alignment using gtf\n  harmonicmean              estimate the harmonic mean from the pangenome\n  pangenome-matcher         pangenome matcher\n  pan-arc                   pangenome annotator\n  snatcher                  extract specific region from paf alignment\n  precomputed-paf           generate stats from precomputed paf\n  precompute-cds            extract the coding regions from the precomputed pangenome\n  graph                     graph analyzer\n  pangenome-bed             Pangenome bed constructor\n  intergenic-noncoding      Intergenic extractor\n  pan-reads-database        pangenome database\n  bedtool-ancestral         analyze pangenome from the bedtools alignment to ancestral state\n  vcf-aanalyze              analyze pangenome vcffiles\n  pangenome-single-merge    merge single pangenome bedfile\n  multi-bedtools-ancestral  bedtools sncestral multi-pangenome\n  help                      Print this message or the help of the given subcommand(s)\n\n Options:\n  -h, --help     Print help\n  -V, --version  Print version \n \n ```\n Gaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fpanscape","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fibchgenomic%2Fpanscape","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fibchgenomic%2Fpanscape/lists"}