{"id":45977488,"url":"https://github.com/koesterlab/microphaser","last_synced_at":"2026-02-28T16:36:35.529Z","repository":{"id":30901698,"uuid":"111705240","full_name":"koesterlab/microphaser","owner":"koesterlab","description":null,"archived":false,"fork":false,"pushed_at":"2022-11-18T15:52:06.000Z","size":2005,"stargazers_count":11,"open_issues_count":4,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2023-03-01T12:50:58.677Z","etag":null,"topics":["phasing","software","variant-calling"],"latest_commit_sha":null,"homepage":null,"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/koesterlab.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}},"created_at":"2017-11-22T16:03:53.000Z","updated_at":"2022-11-17T01:20:13.000Z","dependencies_parsed_at":"2023-01-14T17:55:05.220Z","dependency_job_id":null,"html_url":"https://github.com/koesterlab/microphaser","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"purl":"pkg:github/koesterlab/microphaser","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/koesterlab%2Fmicrophaser","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/koesterlab%2Fmicrophaser/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/koesterlab%2Fmicrophaser/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/koesterlab%2Fmicrophaser/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/koesterlab","download_url":"https://codeload.github.com/koesterlab/microphaser/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/koesterlab%2Fmicrophaser/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29943143,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-28T13:49:17.081Z","status":"ssl_error","status_checked_at":"2026-02-28T13:48:50.396Z","response_time":90,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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"}},"keywords":["phasing","software","variant-calling"],"created_at":"2026-02-28T16:36:32.916Z","updated_at":"2026-02-28T16:36:34.885Z","avatar_url":"https://github.com/koesterlab.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Microphaser\n\nMicrophaser is a tool for phasing small tumor DNA sequences - e.g. coding for small peptides - in linear time.  \nIt can be used in tumor neoantigen prediction to generate the neo-peptidome.\n\n## Installation\n\n  Microphaser is available for installation via conda. \n  Use `conda install -c biconda microphaser` to easily install the current version.\n  \n## Usage\n\n### Input\n  To use microphaser, you need the following input files:\n  \n  * a sorted and indexed bam file containing mapped tumor reads\n  * a reference genome in fasta format\n  * a matching gene and transcript annotation in gtf format\n  * a bcf/vcf file containing germline and somatic variants, where somatic variants should be flagged with a ```SOMATIC``` INFO tag\n  * optional: a bcf/vcf file containing only germline variants\n  \n### Output\n  Microphaser returns three important files:\n\n  * two filtered fasta files containing all neopeptides and their wildtype counterparts for further use with MHC-binding prediction tools\n  * an info file in tsv format containing meta-information about every neopeptide\n  \n  \n  The info table consist of the following fields:\n  * id: peptide identifier as found in the fasta files\n  * transcript: Ensembl transcript name\n  * gene_id: Ensembl gene name\n  * gene_name: Gene symbol\n  * chrom: Chromosome\n  * offset: Position of the neopeptide on the chromosome\n  * freq: Frequency of the neopeptide occurring in all reads overlapping the peptide position\n  * depth: Read depth at the peptide position\n  * nvar: number of variants in the neopeptide\n  * nsomatic: number of somatic variants in the neopeptide\n  * nvariant_sites: number of variant sites in the range of the neopeptide\n  * nsomvariant_sites: number of somatic variant sites in the range of the neopeptide\n  * strand: Strand orientation of the transcript (forward or reverse)\n  * somatic_positions: Positions of the somatic variants in the neopeptide\n  * somatic_aa_change: Somatic Amino Acid changes occuring in the neopeptide\n  * germline_positions: Positions of germline variants in the neopeptide\n  * germline_aa_change: Germline Amino Acid changes occuring in the neopeptide\n  * normal_sequence: Nucleotide sequence of the wildtype peptide\n  * mutant_sequence: Nucleotide sequence of the neopeptide\n  \n### Run\n  \n  Currently, microphaser consists of four different submodules:\n\n  - somatic (returns neopeptides and their corresponding normal peptides)\n  - normal (returns all normal peptides of the patient)\n  - build_reference (returns a binary file representing the patients normal peptidome)\n  - filter (compares neopeptides against the normal peptidome and removes self-similar candidates)\n\n  \n  You can run microphaser like this:\n  \n  Phasing of the tumor reads and variants:\n\n  ```\n  microphaser somatic tumor.bam -r reference.fasta -b all_variants.bcf -t neopeptides.info.tsv -n peptides.wt.fasta \u003c annotation.gtf \u003e peptides.mt.fasta\n  ```\n  \n  Generation of the patients healthy peptidome:\n  \n  ```\n  microphaser normal normal.bam -r reference.fasta -b germline_variants.bcf \u003c annotation.gtf \u003e healthy_peptides.fasta\n  ```\n  \n  Building the reference binary file of the healthy peptidome: \n  \n  ```\n  microphaser build_reference -r healthy_peptides.fasta -o peptides.bin \u003e peptides.translated.fasta\n  ```\n\n  Filtering the neopeptide candidates from subcommand ```microphaser somatic```: \n\n  ```\n  microphaser filter -r peptides.bin -t neopeptides.info.tsv -o neopeptides.filtered.info.tsv -n normal_peptides.filtered.fasta \u003e neopeptides.filtered.fasta\n  ```\n  \n## Authors\n\n* Jan Forster (https://github.com/jafors)\n* Johannes Köster (https://koesterlab.github.io) \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkoesterlab%2Fmicrophaser","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkoesterlab%2Fmicrophaser","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkoesterlab%2Fmicrophaser/lists"}