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      Draft Genome Sequence of the Alkaliphilic, Lithoautotrophic Homoacetogen Fuchsiella alkaliacetigena Z-7100 T

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      Publication date (Electronic, pub):
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      Journal: Microbiology Resource Announcements
      Publisher: American Society for Microbiology

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          ABSTRACT

          Fuchsiella alkaliacetigena is a spore-forming, alkaliphilic hydrogentrophic homoacetogen that was isolated from the soda lake Lake Tanatar III in Russia. The genome of the type strain Z-7100 (= DSM 24880) is 2.9 Mb, with a G+C content of 36.2%.

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          SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

          Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
          The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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            fastp: an ultra-fast all-in-one FASTQ preprocessor

            Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)
            Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.
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              Prokka: rapid prokaryotic genome annotation.

              T Seemann (2014)
              The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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                Author and article information

                Contributors
                Masaru K. Nobu
                Souichiro Kato
                Julia A. Maresca: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, pub): 1 August 2022
                Publication date (Electronic, collection): August 2022
                Publication date PMC-release: 1 August 2022
                Volume: 11
                Issue: 8
                Electronic Location Identifier: e00471-22
                Affiliations
                [a ] Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
                [b ] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
                [c ] Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
                University of Delaware
                Author notes

                The authors declare no conflict of interest.

                Article
                Publisher ID: 00471-22 Publisher ID: mra.00471-22
                DOI: 10.1128/mra.00471-22
                PMC ID: 9387241
                PubMed ID: 35913143
                SO-VID: 1cb752b3-4cb3-4c88-b8c4-38236fff2643
                Copyright © Copyright © 2022 Huang et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 20 May 2022
                Date accepted : 15 July 2022
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 9, Pages: 2, Words: 951
                Funding
                Funded by: JSPS KAKENHI;
                Award ID: JP20H05594
                Award Recipient :
                Funded by: JSPS KAKENHI;
                Award ID: JP18H03367
                Award Recipient :
                Funded by: JST SPRING;
                Award ID: JPMJSP2119
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Compound subject: environmental-microbiology, Environmental Microbiology
                Custom metadata
                cover-date August 2022

                Data availability:

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