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READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

Raeece Naeem, Mamoon Rashid, Arnab Pain
2012 Computer applications in the biosciences : CABIOS  

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READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.  ...  READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in 527 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material).  ...  READSCAN reports the genome relative abundance (GRA) of those identified non-host microbial sequences implemented based on a proven finite mixture model and expectation maximization algorithm (Xia et  ... 
doi:10.1093/bioinformatics/bts684 pmid:23193222 pmcid:PMC3562070 fatcat:k4nlws2hsvcsfonwf6a6uoyi5u
Citation

Raeece Naeem, Mamoon Rashid, Arnab Pain. "READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation." Computer applications in the biosciences : CABIOS 29.3 (2012) 391-392

Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types

Ilya Plyusnin, Ravi Kant, Anne J Jääskeläinen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura
2020 Virus Evolution  

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https://web.archive.org/web/20201205173916/https://watermark.silverchair.com/veaa091.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArAwggKsBgkqhkiG9w0BBwagggKdMIICmQIBADCCApIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMgOm9juLVMQL8xlWvAgEQgIICYyubgCa64n7BCXFP2fijK6ZY0k_ClxZqBnyG4aVce53j3Wyd0X8aHuL0ZLh0_5Pe4N4sRQwebrqVC7jeEKCx4GdzI-KRMjf3NKLisDXnD1en3y8z-AhzbQzc9hecfTVh0oVle-8_NGOhEZlKbJVzujk5mJKBwCBG7wEsI9l3IGcnjuZZion2qY6Ne5rhXQUbX6GuD_hq0Aq0BsSCSp39s4nD6Gnfis6S47bC1zPBxHedpKJ7xUtpKUPEcCI-Fguxt_oZaGx_JhYyyQNjYB1xPDWjErUXmcDEG1ntdVf55BDbyAOhzBMRBrzvmglSJ1gC_5bAh_vy47hTh_MUrHy9zHHkPia7Ens6BwnkGTHCgltsvRy9dKMOLse7-vWHtRKwe3J9MesMzTgxaQBBn2WsQsrrEVVdAdSMdDgvBam6H0lAbcZoY2FdIP5cZr1-jwktID4LFYE35MM71zbWhqPeH6bJQhUgAX8b1YWZuwCcyfliE3rX1mWeiNZHlvKbUT2IRL0kuZiRpX0hcBzvY64gV1W8dwzYqzXgNsNoUKWr9G6CyAa2vIAaixKMBlRlWfoI5LGJCeTYsMKouTq5CFDsFOVDPA7eKsieq7PNcep2-Za1Y3yj11SuxW7LzoQgYXb7xph07Be_zVC-_k0AKdJ67w4SseDs3i8ziUx1SQgRqYm-A72uIpPT9L30YUGEeC4OuVYVJ1m_t6kPxumcwaLiHJnMJncWQxcH_LYMxHSoi-0jmy-W5-EAWgnWZYTynUS4ErLIyzAl0J6UrTZq9H95Xxh7unkzepX3kVamr9OF-pdSxfA4

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discovery based on it.  ...  LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C ++, Perl, and R scripts.  ...  Our pipeline was implemented as a collection of Perl, C++, and R programs with a command-line user interface written in Perl.  ... 
doi:10.1093/ve/veaa091 pmid:33408878 pmcid:PMC7772471 fatcat:nh2g6u7vvngctcdhv2mtajb244
DOAJ
Citation

Ilya Plyusnin, Ravi Kant, Anne J Jääskeläinen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura. "Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types." Virus Evolution 6.2 (2020) veaa091

Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types [article]

Ilya Plyusnin, Ravi Kant, Anne J. Jaaskelainen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura
2020 biorxiv/medrxiv   pre-print

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In this article, we present a novel stand-alone pipeline called LAZYPIPE for identifying both previously known and novel viruses in host-associated or environmental samples and give examples of virus discovery  ...  LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.  ...  These pipelines mine the relative abundance and types of viruses present in a given sample.  ... 
doi:10.1101/2020.05.07.082107 fatcat:63ukgcsq5zgxpffie7zpbz6kje
Citation

Ilya Plyusnin, Ravi Kant, Anne J. Jaaskelainen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura. "Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types." biorxiv/medrxiv (2020)