{"id":18907878,"url":"https://github.com/rennelab/hkref","last_synced_at":"2026-03-06T10:30:24.708Z","repository":{"id":200034733,"uuid":"340213582","full_name":"RenneLab/hkref","owner":"RenneLab","description":"Hybkit-Ref: Up-to-date Genomic Sequence Reference Database for 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(Hybkit-Reference)\n==================================\n.. image:: https://img.shields.io/github/v/release/RenneLab/hkref?include_prereleases\u0026logo=github\n   :target: https://github.com/RenneLab/hkref/releases\n   :alt: GitHub release (latest by date including pre-releases)\n.. image:: https://img.shields.io/badge/Made%20with-Python-1f425f.svg?logo=python\u0026logoColor=white\n   :target: https://www.python.org/\n   :alt: Made with Python\n.. image:: https://img.shields.io/badge/Made%20with-Bash-1f425f.svg?logo=gnu-bash\n   :target: https://www.gnu.org/software/bash/\n   :alt: Made with Bash\n.. image:: https://img.shields.io/badge/Bio-python-yellow?logo=data%3Aimage%2Fpng%3Bbase64%2CiVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAMAAAAoLQ9TAAABvFBMVEUAAAD%2F0UEoaaY3cJ%2F%2F0kD2zUWxq2Zvi4VVgJDvyUlIeJfhwk%2FItlyFlnpBdZs%2Bc5w1b6A4cZ%2F%2F%2FwD%2F0UH%2F0UE3cJ83cJ83cJ83cJ%2F%2F0UL%2F0UD%2F0T%2F%2F0UH%2F0kDXvVQ1b6A3cJ83cJ83cJ83cJ%2F%2Fzzr%2F0kT%2F00j%2F0kT%2F0z%2FMuFk7cp02cJ83cJ83cJ83cJ%2F%2F0UH%2F0UH%2F0kX%2F0kb60ELvykiHl3oAT784cZ43cJ83cJ83cJ%2F%2F0UH%2F0UH%2F0UH%2F0T9YgJDQulf%2B0UH51D43cJ83cJ81b6D%2F4TH%2F0UH%2F0UH%2F0UE3cJ8zbqGJmHn%2F0kD%2F0UE3cJ83cJ80bqDSvFX%2F0kD%2F0UE3cJ82b6BghIz%2F00D%2F0UH%2F0UE2cJ80b6CtqWj%2F0z%2F%2F0UE3cJ83cJ83cJ8YYa7%2F0kD%2F0UH%2F0UFxjIRFd5lnh4nfwlA1bp43cJ83cJ83cJ%2F%2F0UH%2F0UH%2F0UH%2F2Tm%2Fsl9Fd5k7cp08dKI7c6E3cJ83cJ%2F%2F0UH%2F0UH%2F0UH%2F0UH5z0NTfpI0b6A6cqE%2FdaM7cqEwa5z%2F0UH%2F0UH%2F0UH%2F0UH%2F0z8vbKM3cJ81b542cJ84caD%2F0UH%2F0UE3cJ83cJ%2F%2F%2F%2F%2BMZpkLAAAAk3RSTlMAAAAAAAAAAAAAAAAAAAAAAAAAAQUKTlYRBiYNBmYkifDyog4EdORih83qcl7scBzb9lBH%2BrIKA5bYH17tdwxW%2Fa0GMOV0DcOtCAu08Og8AprNa%2BtLSOtuzZsDPOjutwwHqsUOcuYyCbr%2BWQtz7WIe1Z4q3PhHTfTdHWXuhrfVsolh5nkECYTo0UQcaQ0pBiYaBQETquGoAAAAl0lEQVQY02NgIAQYGRiFGN8JMzIyvmb4yygBpBkYpRkh4ME%2FZSDJwsDwQgUiwMDCDRb4z8gNETA%2FwwMWZ2axAFLHrCGiO4BanMEssCzjWgYmZgZuEAjcDaYY%2FrMwxEItASlZxMDAlMHDw7MKKMcJUsD0n4EJTE%2Fi4soAM5ghAl8g5nBzBzCABXr%2F%2Fq%2BZxsFR0cFmxEAEAAAfKxn6VT4rZAAAAABJRU5ErkJggg%3D%3D%0A\n   :target: https://github.com/biopython/biopython\n   :alt: BioPython Project\n.. image:: http://biothings.io/static/img/powered-by-mygene.png\n   :width: 128 px\n   :target: https://mygene.info/\n   :alt: Powered by MyGene.info\n\n| This repository is a part of the `hybkit project \u003chttp://www.github.com/RenneLab/hybkit\u003e`_.\n| Full hybkit project documentation is available at\n  `hybkit's ReadTheDocs \u003chttps://hybkit.readthedocs.io/\u003e`_.\n\nDescription:\n============\n| This repository includes an up-to-date human genomic sequence reference designed to be\n  compaitble with the `Hyb \u003chttps://github.com/gkudla/hyb\u003e`_ program\n  for chimeric (hybrid) read calling for ribonomics experiments.\n| The method for reference library construction is based on the protocol provided in the\n  supplemental methods of:\n\n  | Helwak, Aleksandra, et al. 'Mapping the human miRNA interactome by CLASH reveals\n    frequent noncanonical binding.' Cell 153.3 (2013): 654-665.\n    http://dx.doi.org/10.1016/j.cell.2013.03.043\n\n| The reference library is primarily based on sequences downloaded from Ensembl via the\n  Biomart API, with the use of miRBase for mature miRNA sequences and a few other sequence\n  sources.\n\nBiomart queries include:\n  * mRNA : transcript_biotype=protein_coding; cdna;\n    (limited to where a RefSeq Protein Identifier Exists)\n  * lncRNA : transcript_biotype=lncrna; cdna\n  * rRNA : transcript_biotype=lncrna; cdna\n  * rRNA : transcript_biotype=[Mt_rRNA, rRNA, rRNA_pseudogene]; transcript_exon_intron\n  * tRNA : transcript_biotype=Mt_tRNA; transcript_exon_intron\n  * other : transcript_biotype=[all remaining]; transcript_exon_intron\n\nFor a detailed description of the current sequences and queries utilized, see\n\"Current Reference Details\" below.\n\nRun Reference Creation Pipeline:\n================================\nThe reference pipeline is designed using Nextflow, and has been tested on Nextflow/23.04.1.\nDependency handling is performed with conda modules (containerized implementation\nin development).\n\nRequired program dependencies are:\n  * `nextflow \u003chttps://www.nextflow.io/\u003e`_ (tested v23.04.1)\n  * `seqkit \u003chttps://bioinf.shenwei.me/seqkit/\u003e`_ (tested v2.5.1)\n  * `bedops \u003chttps://bedops.readthedocs.io/en/latest/\u003e`_ (tested v2.4.39)\n\nRequired Python Packages:\n  * `pandas \u003chttps://pandas.pydata.org/\u003e`_ (tested pandas=1.3.5)\n  * `natsort \u003chttps://pypi.org/project/natsort/\u003e`_ (tested natsort=7.1.1)\n  * `pybiomart \u003chttps://pypi.org/project/pybiomart/\u003e`_ (tested pybiomart=0.2.0)\n  * `biothings-client \u003chttps://pypi.org/project/biothings-client/\u003e`_ (tested biothings_client=0.2.6)\n  * `biopython \u003chttps://biopython.org/\u003e`_ (tested biopython=1.79)\n  * `pyyaml \u003chttps://pyyaml.org/\u003e`_ (tested pyyaml=6.0)\n\nThe scripts can be run by executing the first script: \"00_run_all.sh\" using the presupplied\nconda configuration, or by making all required resources (seqkit, python3) available on the system path.\n\nHyb Reference Specification:\n============================\nThe Hyb program has requirements about the formatting of the FASTA file used for the reference.\n\nCurrently identified requirements include:\n  * No description in FASTA sequence header (no whitespace characters)\n  * | Sequence identifier be of the form of \"{1}_{2}_{seqid}_{biotype}\"\n    | {1}: Arbitrary Identifier (ENSG... for Ensembl Sequences)\n    | {2}: Arbitrary Identifier (ENST... for Ensembl Sequences)\n    | {3}: Name of gene/miRNA\n    | {4}: Ensembl-style transcript_biotype.\n    |     (Note, \"microRNA\" must be used in place of \"miRNA\" for recognition by Hyb)\n\n  * {1}, {2}, {seqid}, and {biotype} should contain only [a-z], [A-Z], [0-9],\n     \"-\", and \"|\" characters.\n  * \"_\", \".\", and \",\" characters are *specifically* excluded from identifiers.\n\nExamples:\n\n.. code-block:: bash\n\n    \u003eENSG00000003137_ENST00000001146_CYP26B1_mRNA\n    .....\n    \u003eMIMAT0000062_MirBase_let-7a_microRNA\n    TGAGGTAGTAGGTTGTATAGTT\n\nThanks to Grzegorz Kudla ( https://github.com/gkudla ) for providing information on\nHyb reference creation.\n\nCurrent Reference Details:\n==========================\n\nText of: *./01_notes.sh*\n\n.. code-block:: bash\n\n    Download a reference sequence library for the Hyb program from Ensembl\n    using the Biomart python module.\n\n    Library construction is based on the protocol provided in the supplemental methods of:\n    Helwak, Aleksandra, et al. 'Mapping the human miRNA interactome by CLASH reveals\n    frequent noncanonical binding.' Cell 153.3 (2013): 654-665.\n    http://dx.doi.org/10.1016/j.cell.2013.03.043\n    ( Supplemental methods section found only in PDF-fulltext )\n\n    Biomart queries include:\n      protein_coding (as cDNA)\n      lncRNA (as cDNA)\n      All remaining gene_biotypes\n          as unspliced transcripts ('transcript_exon_intron')\n\n    tRNAs:  genomic tRNA database http://gtrnadb.ucsc.edu/)\n    rRNAs:  NCBI Genbank Database, rRNA sequences (NR_003287.4, NR_003286.4);\n    miRNAs: miRBase release 22.1 (http://www.mirbase.org): mature human miRNAs.\n\n    These sequences are then formatted in the required {}_{}_{name}_{biotype} header\n    format for Hyb, and all extra '.' and '_' symbols are removed.\n\n    Original biotypes from the hOH7 Hyb database are:\n    Ig, lincRNA, microRNA, miscRNA, mRNA, mtrRNA, pr-tr, pseudo, rRNA, snoRNA, snRNA, Trec, tRNA\n    In this version, biotypes are passed through as with the ensembl 'transcript_biotype' field.\n\n    In order to facillitate unambiguous miRNA alignment, mature iRNA sequences are aligned to the\n    reference transcriptome, and any alignemnts within transcripts are masked. This is performed to\n    ensure both that each given miRNA sequence has only a single reference alignment, as well as\n    to allow miRNA precursor transcripts to be identified as hybrid targets.\n\n    \"\"\"\n    echo \"${NOTES}\"\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frennelab%2Fhkref","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frennelab%2Fhkref","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frennelab%2Fhkref/lists"}