{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:31:44Z","timestamp":1740137504838,"version":"3.37.3"},"reference-count":29,"publisher":"World Scientific Pub Co Pte Ltd","issue":"06","funder":[{"name":"Natural Science Foundation of SZU","award":["827-000191"],"award-info":[{"award-number":["827-000191"]}]},{"name":"Natural Science Foundation of SZU","award":["2016091"],"award-info":[{"award-number":["2016091"]}]},{"name":"Guangdong Innovation Research Team Fund","award":["2014ZT05S078"],"award-info":[{"award-number":["2014ZT05S078"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:p> There are many short-read aligners that can map short reads to a reference genome\/sequence, and most of them can directly accept a FASTQ file as the input query file. However, the raw data usually need to be pre-processed. Few software programs specialize in pre-processing raw data generated by a variety of next-generation sequencing (NGS) technologies. Here, we present AUSPP, a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read mapping, and normalized wiggle file creation. It facilitates the processing from raw data to genome mapping and is therefore a powerful tool for the steps before meta-analysis. Most importantly, since AUSPP has default processing pipeline settings for many types of NGS data, most of the time, users will simply need to provide the raw data and genome. AUSPP is portable and easy to install, and the source codes are freely available at https:\/\/github.com\/highlei\/AUSPP . <\/jats:p>","DOI":"10.1142\/s0219720019500379","type":"journal-article","created":{"date-parts":[[2020,2,5]],"date-time":"2020-02-05T03:44:39Z","timestamp":1580874279000},"page":"1950037","source":"Crossref","is-referenced-by-count":3,"title":["AUSPP: A universal short-read pre-processing package"],"prefix":"10.1142","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6488-0292","authenticated-orcid":false,"given":"Lei","family":"Gao","sequence":"first","affiliation":[{"name":"The Key Laboratory of Plant Epigenetics of Guangdong Province, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China"}]},{"given":"Cong","family":"Wu","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Plant Epigenetics of Guangdong Province, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China"}]},{"given":"Lin","family":"Liu","sequence":"additional","affiliation":[{"name":"The Key Laboratory of Plant Epigenetics of Guangdong Province, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China"}]}],"member":"219","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"key":"S0219720019500379BIB001","doi-asserted-by":"publisher","DOI":"10.2144\/000112900"},{"key":"S0219720019500379BIB002","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.05.009"},{"key":"S0219720019500379BIB003","doi-asserted-by":"publisher","DOI":"10.1126\/science.1141319"},{"key":"S0219720019500379BIB004","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth1068"},{"key":"S0219720019500379BIB005","doi-asserted-by":"publisher","DOI":"10.1038\/nature06008"},{"key":"S0219720019500379BIB006","doi-asserted-by":"publisher","DOI":"10.1038\/nature06745"},{"key":"S0219720019500379BIB007","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.03.029"},{"key":"S0219720019500379BIB008","doi-asserted-by":"publisher","DOI":"10.1038\/nature13802"},{"key":"S0219720019500379BIB009","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3645"},{"key":"S0219720019500379BIB010","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1223"},{"key":"S0219720019500379BIB011","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"S0219720019500379BIB012","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"S0219720019500379BIB013","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3317"},{"key":"S0219720019500379BIB014","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn025"},{"key":"S0219720019500379BIB015","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2013-14-4-r36"},{"key":"S0219720019500379BIB017","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.05.004"},{"key":"S0219720019500379BIB019","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu041"},{"key":"S0219720019500379BIB020","doi-asserted-by":"publisher","DOI":"10.1126\/science.1160342"},{"key":"S0219720019500379BIB021","doi-asserted-by":"publisher","DOI":"10.1261\/rna.035279.112"},{"key":"S0219720019500379BIB022","doi-asserted-by":"publisher","DOI":"10.1016\/j.gdata.2015.06.026"},{"key":"S0219720019500379BIB023","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.6157.1"},{"key":"S0219720019500379BIB024","doi-asserted-by":"publisher","DOI":"10.1101\/gr.4086505"},{"key":"S0219720019500379BIB025","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"S0219720019500379BIB026","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"S0219720019500379BIB027","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"S0219720019500379BIB029","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"S0219720019500379BIB030","first-page":"5","volume":"12","author":"Li S","year":"2016","journal-title":"Elife"},{"key":"S0219720019500379BIB031","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1090"},{"key":"S0219720019500379BIB032","doi-asserted-by":"publisher","DOI":"10.1101\/gr.182238.114"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720019500379","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,5]],"date-time":"2020-02-05T03:45:32Z","timestamp":1580874332000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720019500379"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12]]},"references-count":29,"journal-issue":{"issue":"06","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["10.1142\/S0219720019500379"],"URL":"https:\/\/doi.org\/10.1142\/s0219720019500379","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"type":"print","value":"0219-7200"},{"type":"electronic","value":"1757-6334"}],"subject":[],"published":{"date-parts":[[2019,12]]}}}