{"id":4813,"name":"miassembler","description":null,"url":"https://github.com/ebi-metagenomics/miassembler","last_synced_at":"2025-09-04T17:33:24.120Z","repository":{"id":226047231,"uuid":"743551113","full_name":"EBI-Metagenomics/miassembler","owner":"EBI-Metagenomics","description":null,"archived":false,"fork":false,"pushed_at":"2025-08-05T15:25:13.000Z","size":35610,"stargazers_count":4,"open_issues_count":1,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-08-05T17:26:13.282Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/EBI-Metagenomics.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-01-15T13:31:06.000Z","updated_at":"2025-08-01T08:44:28.000Z","dependencies_parsed_at":"2024-05-20T11:43:58.446Z","dependency_job_id":"a9335dcc-d574-4f30-8dd9-bc0ed220288c","html_url":"https://github.com/EBI-Metagenomics/miassembler","commit_stats":null,"previous_names":["ebi-metagenomics/miassembler"],"tags_count":9,"template":false,"template_full_name":null,"purl":"pkg:github/EBI-Metagenomics/miassembler","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/EBI-Metagenomics","download_url":"https://codeload.github.com/EBI-Metagenomics/miassembler/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273644030,"owners_count":25142745,"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","status":"online","status_checked_at":"2025-09-04T02:00:08.968Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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"}},"owner":{"login":"EBI-Metagenomics","name":"MGnify","uuid":"32897658","kind":"organization","description":"MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data","email":"metagenomics-help@ebi.ac.uk","website":"https://www.ebi.ac.uk/metagenomics/","location":"Genome Campus, UK","twitter":"MGnifyDB","company":null,"icon_url":"https://avatars.githubusercontent.com/u/32897658?v=4","repositories_count":153,"last_synced_at":"2024-04-14T09:50:04.266Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/EBI-Metagenomics","funding_links":[],"total_stars":457,"followers":62,"following":0,"created_at":"2022-11-05T16:04:21.288Z","updated_at":"2024-04-14T09:51:05.583Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/EBI-Metagenomics","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/EBI-Metagenomics/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"EBI-Metagenomics/miassembler","html_url":"https://github.com/EBI-Metagenomics/miassembler","last_synced_at":"2025-08-31T13:17:17.505Z","status":null,"issues_count":0,"pull_requests_count":26,"avg_time_to_close_issue":null,"avg_time_to_close_pull_request":228762.68421052632,"issues_closed_count":0,"pull_requests_closed_count":19,"pull_request_authors_count":6,"issue_authors_count":0,"avg_comments_per_issue":null,"avg_comments_per_pull_request":0.3076923076923077,"merged_pull_requests_count":19,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":0,"past_year_pull_requests_count":26,"past_year_avg_time_to_close_issue":null,"past_year_avg_time_to_close_pull_request":228762.68421052632,"past_year_issues_closed_count":0,"past_year_pull_requests_closed_count":19,"past_year_pull_request_authors_count":6,"past_year_issue_authors_count":0,"past_year_avg_comments_per_issue":null,"past_year_avg_comments_per_pull_request":0.3076923076923077,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":19,"created_at":"2025-08-29T11:47:49.351Z","updated_at":"2025-09-03T04:15:08.966Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/EBI-Metagenomics%2Fmiassembler/issues","issue_labels_count":{},"pull_request_labels_count":{"bug":1},"issue_author_associations_count":{"MEMBER":1},"pull_request_author_associations_count":{"MEMBER":39,"CONTRIBUTOR":10,"NONE":4},"issue_authors":{"mberacochea":1},"pull_request_authors":{"mberacochea":21,"Ge94":15,"KateSakharova":7,"ochkalova":4,"jmattock5":3,"SandyRogers":3},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10079913,"issues_count":31291083,"pull_requests_count":96059117,"authors_count":10693123,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"MEMBER":1},"past_year_pull_request_author_associations_count":{"MEMBER":25,"CONTRIBUTOR":10,"NONE":2},"past_year_issue_authors":{"mberacochea":1},"past_year_pull_request_authors":{"mberacochea":11,"Ge94":11,"KateSakharova":5,"ochkalova":4,"jmattock5":3,"SandyRogers":3},"maintainers":[{"login":"mberacochea","count":22,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mberacochea"},{"login":"Ge94","count":15,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Ge94"},{"login":"SandyRogers","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/SandyRogers"}],"active_maintainers":[{"login":"mberacochea","count":12,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mberacochea"},{"login":"Ge94","count":11,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/Ge94"},{"login":"SandyRogers","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/SandyRogers"}]},"events":{"total":{"ReleaseEvent":4,"WatchEvent":1,"DeleteEvent":23,"IssueCommentEvent":12,"PushEvent":122,"PullRequestEvent":57,"PullRequestReviewEvent":183,"PullRequestReviewCommentEvent":207,"CreateEvent":25},"last_year":{"ReleaseEvent":4,"WatchEvent":1,"DeleteEvent":23,"IssueCommentEvent":12,"PushEvent":122,"PullRequestEvent":57,"PullRequestReviewEvent":183,"PullRequestReviewCommentEvent":207,"CreateEvent":25}},"keywords":[],"dependencies":[{"ecosystem":"cpan","filepath":"modules/nf-core/blast/blastn/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.185Z","updated_at":"2024-03-06T23:45:58.185Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/blast/blastn/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/bwamem2/index/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.190Z","updated_at":"2024-03-06T23:45:58.190Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/bwamem2/index/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/custom/dumpsoftwareversions/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.212Z","updated_at":"2024-03-06T23:45:58.212Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/custom/dumpsoftwareversions/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.219Z","updated_at":"2024-03-06T23:45:58.219Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/megahit/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.225Z","updated_at":"2024-03-06T23:45:58.225Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/megahit/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.230Z","updated_at":"2024-03-06T23:45:58.230Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.234Z","updated_at":"2024-03-06T23:45:58.234Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/quast/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.239Z","updated_at":"2024-03-06T23:45:58.239Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/quast/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/samtools/idxstats/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.243Z","updated_at":"2024-03-06T23:45:58.243Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/samtools/idxstats/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqkit/grep/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.255Z","updated_at":"2024-03-06T23:45:58.255Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/seqkit/grep/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/seqkit/seq/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.260Z","updated_at":"2024-03-06T23:45:58.260Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/seqkit/seq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/spades/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.264Z","updated_at":"2024-03-06T23:45:58.264Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/spades/meta.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2024-03-06T23:45:58.362Z","updated_at":"2024-03-06T23:45:58.362Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/ebi-metagenomics/bwamem2/mem/meta.yml","sha":null,"kind":"manifest","created_at":"2024-04-22T11:48:39.584Z","updated_at":"2024-04-22T11:48:39.584Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/ebi-metagenomics/bwamem2/mem/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/ebi-metagenomics/samtools/bam2fq/meta.yml","sha":null,"kind":"manifest","created_at":"2024-04-22T11:48:39.884Z","updated_at":"2024-04-22T11:48:39.884Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/ebi-metagenomics/samtools/bam2fq/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastp/meta.yml","sha":null,"kind":"manifest","created_at":"2024-04-22T11:48:40.049Z","updated_at":"2024-04-22T11:48:40.049Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/fastp/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/ebi-metagenomics/reads_bwamem2_decontamination/meta.yml","sha":null,"kind":"manifest","created_at":"2024-04-22T11:48:40.735Z","updated_at":"2024-04-22T11:48:40.735Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/subworkflows/ebi-metagenomics/reads_bwamem2_decontamination/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/blast/blastn/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:46.718Z","updated_at":"2024-05-20T11:43:46.718Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/blast/blastn/environment.yml","dependencies":[{"id":18178889314,"package_name":"blast","ecosystem":"conda","requirements":"2.14.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/bwamem2/index/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:47.157Z","updated_at":"2024-05-20T11:43:47.157Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/bwamem2/index/environment.yml","dependencies":[{"id":18178889399,"package_name":"bwa-mem2","ecosystem":"conda","requirements":"2.2.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/custom/dumpsoftwareversions/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:47.826Z","updated_at":"2024-05-20T11:43:47.826Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/custom/dumpsoftwareversions/environment.yml","dependencies":[{"id":18178889400,"package_name":"multiqc","ecosystem":"conda","requirements":"1.17.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/fastqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:47.879Z","updated_at":"2024-05-20T11:43:47.879Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/fastqc/environment.yml","dependencies":[{"id":18178889401,"package_name":"fastqc","ecosystem":"conda","requirements":"0.12.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/megahit/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:48.410Z","updated_at":"2024-05-20T11:43:48.410Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/megahit/environment.yml","dependencies":[{"id":18178889734,"package_name":"megahit","ecosystem":"conda","requirements":"1.2.9.*","direct":true,"kind":"runtime","optional":false},{"id":18178890116,"package_name":"pigz","ecosystem":"conda","requirements":"2.6.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:48.759Z","updated_at":"2024-05-20T11:43:48.759Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml","dependencies":[{"id":18178890140,"package_name":"metabat2","ecosystem":"conda","requirements":"2.15.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:49.400Z","updated_at":"2024-05-20T11:43:49.400Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/multiqc/environment.yml","dependencies":[{"id":18178891602,"package_name":"multiqc","ecosystem":"conda","requirements":"1.18.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/quast/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:49.851Z","updated_at":"2024-05-20T11:43:49.851Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/quast/environment.yml","dependencies":[{"id":18178891615,"package_name":"quast","ecosystem":"conda","requirements":"5.2.0.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/samtools/idxstats/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:50.862Z","updated_at":"2024-05-20T11:43:50.862Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/samtools/idxstats/environment.yml","dependencies":[{"id":18178891635,"package_name":"samtools","ecosystem":"conda","requirements":"1.18.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/seqkit/grep/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:51.018Z","updated_at":"2024-05-20T11:43:51.018Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/seqkit/grep/environment.yml","dependencies":[{"id":18178891638,"package_name":"seqkit","ecosystem":"conda","requirements":"2.4.0.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/seqkit/seq/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:51.506Z","updated_at":"2024-05-20T11:43:51.506Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/seqkit/seq/environment.yml","dependencies":[{"id":18178891645,"package_name":"seqkit","ecosystem":"conda","requirements":"2.6.1.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/spades/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:51.679Z","updated_at":"2024-05-20T11:43:51.679Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/nf-core/spades/environment.yml","dependencies":[{"id":18178891649,"package_name":"spades","ecosystem":"conda","requirements":"3.15.5.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"modules/ebi-metagenomics/bwamem2/mem/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:52.577Z","updated_at":"2024-05-20T11:43:52.577Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/ebi-metagenomics/bwamem2/mem/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/ebi-metagenomics/samtools/bam2fq/environment.yml","sha":null,"kind":"manifest","created_at":"2024-05-20T11:43:52.650Z","updated_at":"2024-05-20T11:43:52.650Z","repository_link":"https://github.com/EBI-Metagenomics/miassembler/blob/main/modules/ebi-metagenomics/samtools/bam2fq/environment.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:50:12.953Z","updated_at":"2025-10-07T08:05:11.040Z","avatar_url":"https://github.com/EBI-Metagenomics.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1371/journal.pone.0163962","https://doi.org/10.1093/bioinformatics/btu153"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/4813","html_url":"https://science.ecosyste.ms/projects/4813","bibtex_url":"https://science.ecosyste.ms/projects/4813/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/4813/export.apalike"}