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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  
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

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  
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

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
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