Using SPAdes De Novo Assembler. Issue 1 (19th June 2020)
- Record Type:
- Journal Article
- Title:
- Using SPAdes De Novo Assembler. Issue 1 (19th June 2020)
- Main Title:
- Using SPAdes De Novo Assembler
- Authors:
- Prjibelski, Andrey
Antipov, Dmitry
Meleshko, Dmitry
Lapidus, Alla
Korobeynikov, Anton - Editors:
- Baxevanis, Andreas D.
Petsko, Gregory A.
Stein, Lincoln D.
Stormo, Gary D. - Abstract:
- Abstract: SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1 : Assembling isolate bacterial datasets Basic Protocol 2 : Assembling metagenomic datasets Basic Protocol 3 : Assembling sets of putative plasmids Basic Protocol 4 : Assembling transcriptomes Basic Protocol 5 : Assembling putative biosynthetic gene clusters Support Protocol 1 : Installing SPAdes Support Protocol 2 : Providing input via command line Support Protocol 3 : Providing input data via YAML format Support Protocol 4 : Restarting previous run Support Protocol 5 : Determining strand‐specificity of RNA‐seq data
- Is Part Of:
- Current protocols in bioinformatics. Volume 70:Issue 1(2020)
- Journal:
- Current protocols in bioinformatics
- Issue:
- Volume 70:Issue 1(2020)
- Issue Display:
- Volume 70, Issue 1 (2020)
- Year:
- 2020
- Volume:
- 70
- Issue:
- 1
- Issue Sort Value:
- 2020-0070-0001-0000
- Page Start:
- n/a
- Page End:
- n/a
- Publication Date:
- 2020-06-19
- Subjects:
- biosynthetic gene clusters -- de novo assembly -- genome assembly -- metagenomes -- plasmids -- transcriptome
Bioinformatics -- Laboratory manuals
Nucleotide sequence -- Laboratory manuals
Amino acid sequence -- Laboratory manuals
Base Sequence
Amino Acid Sequence
Computational Biology -- methods
Databases, Genetic
Proteins -- analysis
Sequence Analysis -- methods
Sequence Homology
Amino acid sequence
Bioinformatics
Nucleotide sequence
Laboratory Manuals
Laboratory manuals
570.285 - Journal URLs:
- https://currentprotocols.onlinelibrary.wiley.com/journal/1934340x ↗
http://www3.interscience.wiley.com/cgi-bin/mrwhome/104554769/HOME ↗
http://onlinelibrary.wiley.com/ ↗ - DOI:
- 10.1002/cpbi.102 ↗
- Languages:
- English
- ISSNs:
- 1934-3396
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
British Library HMNTS - ELD Digital store - Ingest File:
- 22317.xml