{"id":18669999,"url":"https://github.com/blahah/idba_tran","last_synced_at":"2025-11-06T18:30:35.300Z","repository":{"id":32489206,"uuid":"36069698","full_name":"blahah/idba_tran","owner":"blahah","description":"Mirror of IDBA tran to provide a stable location for binary distribution","archived":false,"fork":false,"pushed_at":"2015-05-22T12:19:09.000Z","size":344,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-27T19:13:30.740Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/blahah.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-05-22T11:52:32.000Z","updated_at":"2015-05-22T12:02:30.000Z","dependencies_parsed_at":"2022-09-12T15:00:14.373Z","dependency_job_id":null,"html_url":"https://github.com/blahah/idba_tran","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fidba_tran","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fidba_tran/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fidba_tran/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/blahah%2Fidba_tran/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/blahah","download_url":"https://codeload.github.com/blahah/idba_tran/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239500961,"owners_count":19649367,"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":"2024-11-07T08:49:26.212Z","updated_at":"2025-11-06T18:30:35.265Z","avatar_url":"https://github.com/blahah.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"###############################################################################\nCopyright (C) 2009 Yu Peng (ypeng@cs.hku.hk)\n\nThis program is free software; you can redistribute it and/or\nmodify it under the terms of the GNU General Public License\nas published by the Free Software Foundation; either version 2\nof the License, or (at your option) any later version.\n\nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n\nYou should have received a copy of the GNU General Public License\nalong with this program; if not, write to the Free Software\nFoundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.\n\nYu Peng (ypeng@cs.hku.hk)\nDept. of Computer Science,\nThe University of Hong Kong,\nPokfulam Road,\nHong Kong,\nChina\n###############################################################################\n\nRequirement\n\nThis software is suitable for all unix-like system with gcc installed.\n\n\nInstallation Guide\n\nExract the package, then use make to compile the source code.\n$ ./configure\n$ make\n\n\nIntroduction\n\nIDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. \nIDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth \nregions and use progressive depth on contigs to reduce errors in high-depth regions. It is a \ngeneric purpose assembler and epspacially good for single-cell and metagenomic sequencing data. \nIDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference \ngenome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for \nRNA-Seq data.\n\nThe basic IDBA is included for comparison, you should use more specific assemblers for your data.\nIf you are assembling genomic data without reference, please use IDBA-UD.\nIf you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.\nIf you are assembling transcriptome data, please use IDBA-Tran.\n\n\nComments\n\nNote that IDBA assemblers are designed for short reads (around 100bp). If you want to assemble \npaired-end reads with longer read length, please modify the constant kMaxShortSequence in \nsrc/sequence/short_sequence.h to support longer read length.\n\nPlease find the manual by running the assembler without any parameters. For example:\n$ bin/idba\n\nIDBA series assemblers accept fasta format reads. Fastq format reads can be converted by \nfq2fa program in the packcage.\n$ bin/fq2fa read.fq read.fa\n\nIDBA-UD IDBA-Hybrid and IDBA-Tran require paired-end reads stored in single FastA file and a pair of\nreads is in consecutive two lines. If not, please use fq2fa to merge two\nFastQ read files to single file.\n$ bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa\nor convert a FastQ read file to FastA file.\n$ bin/fq2fa --paired --filter read.fq read.fa\n\nThe this tools assume the paired-end reads are in order (-\u003e, \u003c-). If your data is in order (\u003c-, -\u003e), \nplease convert it by yourself.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fidba_tran","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fblahah%2Fidba_tran","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fblahah%2Fidba_tran/lists"}