{"id":20153588,"url":"https://github.com/seqan/dream_yara","last_synced_at":"2026-04-18T00:32:23.294Z","repository":{"id":49722965,"uuid":"353001429","full_name":"seqan/dream_yara","owner":"seqan","description":"DREAM-Yara - An exact read mapper for very large databases with short update time","archived":false,"fork":false,"pushed_at":"2021-06-11T15:45:21.000Z","size":153482,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":5,"default_branch":"master","last_synced_at":"2026-02-11T02:26:37.374Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/seqan.png","metadata":{"files":{"readme":"README.rst","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":"2021-03-30T12:57:19.000Z","updated_at":"2025-11-22T02:20:36.000Z","dependencies_parsed_at":"2022-09-07T01:40:12.033Z","dependency_job_id":null,"html_url":"https://github.com/seqan/dream_yara","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/seqan/dream_yara","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream_yara","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream_yara/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream_yara/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream_yara/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/dream_yara/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fdream_yara/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31951322,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-17T17:29:20.459Z","status":"ssl_error","status_checked_at":"2026-04-17T17:28:47.801Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":[],"created_at":"2024-11-13T23:19:49.007Z","updated_at":"2026-04-18T00:32:23.268Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"DREAM-Yara: An exact read mapper for very large databases with short update time\n===================================================================================\n\nOverview\n--------\nYara is an *exact* tool for aligning DNA sequencing reads to reference genomes.\nDREAM-Yara is an extension of Yara to support distributed read mapping.\nIt works by spliting a given reference database in to smaller manageble partitions\nand this allows faster indexing and super fast updating time.\nDREAM-Yara can quickly exclude reads for parts of the databases where they cannot match.\nThis allows us to keep the databases in several indices which can be easily rebuilt\nif parts are updated while maintaining a fast search time.\nBoth Yara and DREAM-Yara are fully sensitive read mappers.\n\n\nMain features\n~~~~~~~~~~~~~\n\n* Exhaustive enumeration of sub-*optimal* end-to-end alignments under the edit distance.\n* Excellent speed, memory footprint and accuracy.\n* Accurate mapping quality computation.\n* Support for reference genomes consisiting of million of contigs.\n* Direct output in SAM/BAM format.\n\nSupported data\n~~~~~~~~~~~~~~\n\nDREAM-Yara has been tested on DNA reads (i.e., Whole Genome, Exome, ChIP-seq, MeDIP-seq) produced by the following sequencing platforms:\n\n* Illumina GA II, HiSeq and MiSeq (single-end and paired-end).\n* Life Technologies Ion Torrent Proton and PGM.\n\nQuality trimming is *necessary* for Ion Torrent reads and recommended for Illumina reads.\n\nUnsupported data\n~~~~~~~~~~~~~~~~\n\n* RNA-seq reads spanning splicing sites.\n* Long noisy reads (e.g., Pacific Biosciences RSII, Oxford Nanopore MinION).\n\nInstallation from sources\n-------------------------\n\nThe following instructions assume Linux or OS X. For more information, including Windows instructions, refer to the `SeqAn getting started tutorial \u003chttp://trac.seqan.de/wiki/Tutorial/GettingStarted\u003e`_.\n\nSoftware requirements\n~~~~~~~~~~~~~~~~~~~~~\n\n**A modern C++11 compiler with OpenMP 3.0 extensions is required to build Yara. If unsure, use GNU G++ 4.9 or newer.**\n\n* Git.\n* CMake 3.2 or newer.\n* G++ 4.9 or newer.\n\nDownload\n~~~~~~~~\n\nDREAM-Yara sources downloaded by executing:\n\n::\n\n  $ git clone --recurse-submodules https://github.com/seqan/dream_yara.git\n\nConfiguration\n~~~~~~~~~~~~~\n\nCreate a build project by executing CMake as follows:\n\n::\n\n  $ mkdir build\n  $ cd build\n  $ cmake ../dream_yara\n\nBuild\n~~~~~\n\nInvoke make as follows:\n\n::\n\n  $ make all\n\nInstallation\n~~~~~~~~~~~~\n\nCopy the binaries to a folder in your *PATH*, e.g.:\n\n::\n\n  # cp bin/* /usr/local/bin\n\n\nUsage\n-----\n\n\nDistributed Indexer\n~~~~~~~~~~~~~~~~~~~\n\nHere we rquire a refence database splited in to many bins. This can be achieved (eg.) by using TaxSBP from https://github.com/pirovc/taxsbp\n\n::\n\n  $ git clone https://github.com/pirovc/taxsbp\n\n\n\nCreate 64 fasta files under GENOMES_DIR/ directory with names 0-63.fasta\n\n::\n\n  $ dream_yara_build_filter --threads 8 --kmer-size 18 --filter-type bloom --bloom-size 16 --num-hash 3 --output-file IBF.filter GENOMES_DIR/*.fasta\n  $ dream_yara_indexer --threads 8 --output-prefix INDICES_DIR/ GENOMES_DIR/*.fasta\n\nDistributed Mapper\n~~~~~~~~~~~~~~~~~~\n\nSingle-end reads\n^^^^^^^^^^^^^^^^\n\nMap single-end DNA reads on the indexed reference genome by executing:\n\n::\n\n  $ dream_yara_mapper -t 8 -ft bloom -e 0.03 -fi IBF.filter -o READS.bam INDICES_DIR/ READS.fastq.gz\n\nPaired-end reads\n^^^^^^^^^^^^^^^^\n\nMap paired-end reads by providing two DNA read files:\n\n::\n\n  $ dream_yara_mapper -t 8 -ft bloom -e 0.03 -fi IBF.filter -o READS.bam INDICES_DIR/ READS_1.fastq.gz READS2.fastq.gz\n\n\nOutput format\n^^^^^^^^^^^^^\n\nOutput files follow the `SAM/BAM format specification \u003chttp://samtools.github.io/hts-specs/SAMv1.pdf\u003e`_.\nIn addition, Yara generates the following optional tags:\n\n+-----+----------------------------------------------------+\n| Tag | Meaning                                            |\n+=====+====================================================+\n| NM  | Edit distance                                      |\n+-----+----------------------------------------------------+\n| X0  | Number of co-optimal mapping locations             |\n+-----+----------------------------------------------------+\n| X1  | Number of sub-optimal mapping locations            |\n+-----+----------------------------------------------------+\n| XA  | Alternative locations: (chr,begin,end,strand,NM;)* |\n+-----+----------------------------------------------------+\n\n\nContact\n-------\n\nFor questions or comments, feel free to contact: Temesgen H. Dadi \u003ctemesgen.dadi@fu-berlin.de\u003e\n\n\nReferences\n----------\nDadi, T. H., Siragusa, E., Piro, V. C., Andrusch, A., Seiler, E., Renard, B. Y., \u0026 Reinert, K. (2018).\nDREAM-Yara: an exact read mapper for very large databases with short update time, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i766–i772, https://doi.org/10.1093/bioinformatics/bty567\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fdream_yara","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fdream_yara","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fdream_yara/lists"}