MOTIVATION: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol uses a circularization-based strategy that leaves behind 38-bp adapter sequences, which must be computationally removed from the data. While 'adapter trimming' is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary. RESULTS: We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. For bacterial data, we show that aggregating these datasets allows a single NMP library to yield an assembly whose quality compares favourably to that obtained from regular paired-end reads. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/sequencing/NxTrim
MOTIVATION: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol uses a circularization-based strategy that leaves behind 38-bp adapter sequences, which must be computationally removed from the data. While 'adapter trimming' is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary. RESULTS: We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. For bacterial data, we show that aggregating these datasets allows a single NMP library to yield an assembly whose quality compares favourably to that obtained from regular paired-end reads. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/sequencing/NxTrim
Authors: Natalia E Gogoleva; Yevgeny A Nikolaichik; Timur T Ismailov; Vladimir Y Gorshkov; Vera I Safronova; Andrey A Belimov; Yuri Gogolev Journal: 3 Biotech Date: 2019-02-19 Impact factor: 2.406
Authors: Martin F Arlt; Sountharia Rajendran; Sandra N Holmes; Kathleen Wang; Ingrid L Bergin; Samreen Ahmed; Thomas E Wilson; Thomas W Glover Journal: Environ Mol Mutagen Date: 2018-09-15 Impact factor: 3.216
Authors: Timothy R Fallon; Sarah E Lower; Ching-Ho Chang; Manabu Bessho-Uehara; Gavin J Martin; Adam J Bewick; Megan Behringer; Humberto J Debat; Isaac Wong; John C Day; Anton Suvorov; Christian J Silva; Kathrin F Stanger-Hall; David W Hall; Robert J Schmitz; David R Nelson; Sara M Lewis; Shuji Shigenobu; Seth M Bybee; Amanda M Larracuente; Yuichi Oba; Jing-Ke Weng Journal: Elife Date: 2018-10-16 Impact factor: 8.140
Authors: Miguel Desmarais; Serena Fraraccio; Iva Dolinova; Jakub Ridl; Hynek Strnad; Hana Kubatova; Alena Sevcu; Jachym Suman; Michal Strejcek; Ondrej Uhlik Journal: Antonie Van Leeuwenhoek Date: 2022-06-15 Impact factor: 2.158
Authors: Sandra Wiegand; Mareike Jogler; Christian Boedeker; Daniela Pinto; John Vollmers; Elena Rivas-Marín; Timo Kohn; Stijn H Peeters; Anja Heuer; Patrick Rast; Sonja Oberbeckmann; Boyke Bunk; Olga Jeske; Anke Meyerdierks; Julia E Storesund; Nicolai Kallscheuer; Sebastian Lücker; Olga M Lage; Thomas Pohl; Broder J Merkel; Peter Hornburger; Ralph-Walter Müller; Franz Brümmer; Matthias Labrenz; Alfred M Spormann; Huub J M Op den Camp; Jörg Overmann; Rudolf Amann; Mike S M Jetten; Thorsten Mascher; Marnix H Medema; Damien P Devos; Anne-Kristin Kaster; Lise Øvreås; Manfred Rohde; Michael Y Galperin; Christian Jogler Journal: Nat Microbiol Date: 2019-11-18 Impact factor: 17.745
Authors: Caroline C Kim; Genelle R Healey; William J Kelly; Mark L Patchett; Zoe Jordens; Gerald W Tannock; Ian M Sims; Tracey J Bell; Duncan Hedderley; Bernard Henrissat; Douglas I Rosendale Journal: ISME J Date: 2019-02-06 Impact factor: 10.302