TRTools: a toolkit for genome-wide analysis of tandem repeats
Abstract Summary A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of...
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| Veröffentlicht in: | Bioinformatics 2021-05, Vol.37 (5), p.731-733 |
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| container_title | Bioinformatics |
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| creator | Mousavi, Nima Margoliash, Jonathan Pusarla, Neha Saini, Shubham Yanicky, Richard Gymrek, Melissa |
| description | Abstract
Summary
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.
Availability and implementation
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.
Supplementary information
Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btaa736 |
| format | Article |
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Summary
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.
Availability and implementation
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>ISSN: 1367-4811</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btaa736</identifier><identifier>PMID: 32805020</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Applications Notes ; Documentation ; Gene Library ; Genotype ; Software ; Tandem Repeat Sequences</subject><ispartof>Bioinformatics, 2021-05, Vol.37 (5), p.731-733</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c456t-8b8b7839d355b6b2c959a279d7a99b7a2de043c9dc97d1d01c4e31ec8ef069cc3</citedby><cites>FETCH-LOGICAL-c456t-8b8b7839d355b6b2c959a279d7a99b7a2de043c9dc97d1d01c4e31ec8ef069cc3</cites><orcidid>0000-0002-6086-3903</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097685/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097685/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btaa736$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32805020$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Schwartz, Russell</contributor><creatorcontrib>Mousavi, Nima</creatorcontrib><creatorcontrib>Margoliash, Jonathan</creatorcontrib><creatorcontrib>Pusarla, Neha</creatorcontrib><creatorcontrib>Saini, Shubham</creatorcontrib><creatorcontrib>Yanicky, Richard</creatorcontrib><creatorcontrib>Gymrek, Melissa</creatorcontrib><title>TRTools: a toolkit for genome-wide analysis of tandem repeats</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Summary
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.
Availability and implementation
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><subject>Applications Notes</subject><subject>Documentation</subject><subject>Gene Library</subject><subject>Genotype</subject><subject>Software</subject><subject>Tandem Repeat Sequences</subject><issn>1367-4803</issn><issn>1367-4811</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkF9LwzAUxYMobk6_wuijL3VJk7SNoCDDfyAIMp9DmtzOaNvUJlX27e3YHO7Np3vgnvO7l4PQlOALggWdFdbZpnRdrYLVflYEpTKaHqAxYSmOE8zF4aBpmsUsx3SETrx_x5gTxtgxGtEkxxwneIyuFi8L5yp_GakoDOLDhmjARktoXA3xtzUQqUZVK2995MooqMZAHXXQggr-FB2VqvJwtp0T9Hp3u5g_xE_P94_zm6dYM56GOC_yIsupMJTzIi0SLbhQSSZMpoQoMpUYwIxqYbTIDDGYaAaUgM6hxKnQmk7Q9Ybb9kUNRkMTOlXJtrO16lbSKSv3N419k0v3JXMssjTnA-B8C-jcZw8-yNp6DVWlGnC9lwmjnIiEkLU13Vh157zvoNydIViuu5f73ctt90Nw-vfJXey37MFANgbXt_-F_gCuCpjl</recordid><startdate>20210505</startdate><enddate>20210505</enddate><creator>Mousavi, Nima</creator><creator>Margoliash, Jonathan</creator><creator>Pusarla, Neha</creator><creator>Saini, Shubham</creator><creator>Yanicky, Richard</creator><creator>Gymrek, Melissa</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-6086-3903</orcidid></search><sort><creationdate>20210505</creationdate><title>TRTools: a toolkit for genome-wide analysis of tandem repeats</title><author>Mousavi, Nima ; Margoliash, Jonathan ; Pusarla, Neha ; Saini, Shubham ; Yanicky, Richard ; Gymrek, Melissa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c456t-8b8b7839d355b6b2c959a279d7a99b7a2de043c9dc97d1d01c4e31ec8ef069cc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Applications Notes</topic><topic>Documentation</topic><topic>Gene Library</topic><topic>Genotype</topic><topic>Software</topic><topic>Tandem Repeat Sequences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mousavi, Nima</creatorcontrib><creatorcontrib>Margoliash, Jonathan</creatorcontrib><creatorcontrib>Pusarla, Neha</creatorcontrib><creatorcontrib>Saini, Shubham</creatorcontrib><creatorcontrib>Yanicky, Richard</creatorcontrib><creatorcontrib>Gymrek, Melissa</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Mousavi, Nima</au><au>Margoliash, Jonathan</au><au>Pusarla, Neha</au><au>Saini, Shubham</au><au>Yanicky, Richard</au><au>Gymrek, Melissa</au><au>Schwartz, Russell</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>TRTools: a toolkit for genome-wide analysis of tandem repeats</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2021-05-05</date><risdate>2021</risdate><volume>37</volume><issue>5</issue><spage>731</spage><epage>733</epage><pages>731-733</pages><issn>1367-4803</issn><issn>1367-4811</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Summary
A rich set of tools have recently been developed for performing genome-wide genotyping of tandem repeats (TRs). However, standardized tools for downstream analysis of these results are lacking. To facilitate TR analysis applications, we present TRTools, a Python library and suite of command line tools for filtering, merging and quality control of TR genotype files. TRTools utilizes an internal harmonization module, making it compatible with outputs from a wide range of TR genotypers.
Availability and implementation
TRTools is freely available at https://github.com/gymreklab/TRTools. Detailed documentation is available at https://trtools.readthedocs.io.
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32805020</pmid><doi>10.1093/bioinformatics/btaa736</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0002-6086-3903</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Bioinformatics, 2021-05, Vol.37 (5), p.731-733 |
| issn | 1367-4803 1367-4811 1460-2059 1367-4811 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8097685 |
| source | Oxford Journals Open Access Collection |
| subjects | Applications Notes Documentation Gene Library Genotype Software Tandem Repeat Sequences |
| title | TRTools: a toolkit for genome-wide analysis of tandem repeats |
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