Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Luo, Ruibang; Liu, Binghang; Xie, Yinlong; Li, Zhenyu; Huang, Weihua; Yuan, Jianying; He, Guangzhu; Chen, Yanxiang; Pan, Qi; Liu, Yunjie; Tang, Jingbo; Wu, Gengxiong; Zhang, Hao; Shi, Yujian; Liu, Yong; Yu, Chang; Wang, Bo; Lu, Yao; Han, Changlei; Cheung, David W.; Yiu, Siu Ming; Peng, Shaoliang; Zhu, Xinhua; Liu, Guangming; Liao, Xiangke; Li, Yingrui; Yang, Huanming; Wang, Jian; Lam, Tak Wah; Wang, Jun

doi:10.1186/s13742-015-0069-2

Cited by 199 publications

(139 citation statements)

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“…The quality of the reads was checked using FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and was preprocessed using Trimmomatic v0.30 for paired-end sequencing (6) and NextClip v1.3 for mate pair sequencing (7). The reads were assembled using Canu v1.6 for PacBio reads (8) and SOAPdenovo v2.04 for Illumina reads (9) and were merged using HaploMerger2 v.20151124 (10). The draft genome of H.…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of the Aquatic Fungus Hymenoscyphus tetracladius Strain NNIBRFG329

Goh

Mun

et al. 2018

Microbiol Resour Announc

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Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of the Aquatic Fungus Hymenoscyphus tetracladius Strain NNIBRFG329

Goh

Mun

et al. 2018

Microbiol Resour Announc

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“…A total of 3,051,328 reads and 762,832,000 clean bases were generated and were assembled into 311 contigs (171con-tigs of Ն1,000 bp) with an N 50 length of 110,446 bp using the SOAPdenovo program (20). Plasmid finishing was achieved by a PCR-based strategy and Sanger sequencing.…”

mentioning

confidence: 99%

MCR-1.6, a New MCR Variant Carried by an IncP Plasmid in a Colistin-Resistant Salmonella enterica Serovar Typhimurium Isolate from a Healthy Individual

Lü

Luo

et al. 2017

Antimicrob Agents Chemother

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In this study, we report a novel mcr-1 gene variant, named mcr-1.6, carried by an IncP plasmid in a colistin-resistant Salmonella enterica serovar Typhimurium isolate from a healthy person. Compared with mcr-1, the mcr-1.6 gene contains two single-nucleotide polymorphisms, one of which results in an arginine to histidine variation (Arg536¡His). The plasmid carrying the mcr-1.6 gene was designated pMCR1.6_P053 and is similar to a recently discovered mcr-1-bearing plasmid found in Klebsiella pneumoniae.

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“…We subjected the publication to a number of data models including ISA-TAB, Research Object, and Nanopublications and despite managing to exactly recreate all of the results listed in the paper, it identified a small number of inaccuracies in the interpretation and discussion [27]. Due to these deficiencies being uncovered, the authors produced a correction article to officially communicate the amendment to their initial report [50]. The open, detailed and transparent approach to reviewing data and methods used by GigaScience has also uncovered methodological problems in companion papers published in other journals.…”

Section: Lessons Learned In Reproducible Data Publishingmentioning

confidence: 99%

Experiences in integrated data and research object publishing using GigaDB

Edmunds

Hunter

et al. 2016

Int J Digit Libr

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In the era of computation and data-driven research, traditional methods of disseminating research are no longer fit-for-purpose. New approaches for disseminating data, methods and results are required to maximize knowledge discovery. The "long tail" of small, unstructured datasets is well catered for by a number of general-purpose repositories, but there has been less support for "big data". Outlined here are our experiences in attempting to tackle the gaps in publishing large-scale, computationally intensive research.GigaScience is an open-access, open-data journal aiming to revolutionize large-scale biological data dissemination, organization and re-use. Through use of the data handling infrastructure of the genomics centre BGI, GigaScience links standard manuscript publication with an integrated database (GigaDB) that hosts all associated data, and provides additional data analysis tools and computing resources. Furthermore, the supporting workflows and methods are also integrated to make published articles more transparent and open. GigaDB has released many new and previously unpublished datasets and data types, including as urgently needed data to tackle infectious disease outbreaks, cancer and the growing food crisis. Other "executable" research objects, such as workflows, virtual machines and software from several GigaScience articles have been archived and shared in reproducible, transparent and usable formats. With data citation producing evidence Office for National Statistics, Duffryn, Government Buildings, Cardiff Rd, Newport NP10 8XG, UK of, and credit for, its use in the wider research community, GigaScience demonstrates a move towards more executable publications. Here data analyses can be reproduced and built upon by users without coding backgrounds or heavy computational infrastructure in a more democratized manner.

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Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Cited by 199 publications

References 2 publications

Draft Genome Sequence of the Aquatic Fungus Hymenoscyphus tetracladius Strain NNIBRFG329

Draft Genome Sequence of the Aquatic Fungus Hymenoscyphus tetracladius Strain NNIBRFG329

MCR-1.6, a New MCR Variant Carried by an IncP Plasmid in a Colistin-Resistant Salmonella enterica Serovar Typhimurium Isolate from a Healthy Individual

Experiences in integrated data and research object publishing using GigaDB

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