We recommend to run SPAdes with BayesHammer/IonHammer to obtain high-quality assemblies. MismatchCorrector - a tool which improves mismatch and short indel rates in resulting contigs and scaffolds this module uses the BWA tool MismatchCorrector is turned off by default, but we recommend to turn it on (see SPAdes options section).SPAdes - iterative short-read genome assembly module values of K are selected automatically based on the read length and data set type.IonHammer - read error correction tool for IonTorrent data, which also works on both types of data.BayesHammer - read error correction tool for Illumina reads, which works well on both single-cell and standard data sets.SPAdes comes in several separate modules: To learn options of these tools you can either run them without any parameters or read this section. In addition, we provide several stand-alone binaries with relatively simple command-line interface: k-mer counting ( spades-kmercounter), assembly graph construction ( spades-gbuilder) and long read to graph aligner ( spades-gmapper). truSPAdes - (DEPRECATED) a module for TruSeq barcode assembly (see truSPAdes manual).coronaSPAdes is a special mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.rnaviralSPAdes - a de novo assembler tailored for RNA viral datasets (transcriptome, metatranscriptome and metavirome).biosyntheticSPAdes - a module for biosynthetic gene cluster assembly with paired-end reads (see biosynthicSPAdes options).rnaSPAdes - a de novo transcriptome assembler from RNA-Seq data (see rnaSPAdes manual).metaplasmidSPAdes - a pipeline for extracting and assembling plasmids from metagenomic data sets (see plasmid options).plasmidSPAdes - a pipeline for extracting and assembling plasmids from WGS data sets (see plasmid options).metaSPAdes - a pipeline for metagenomic data sets (see metaSPAdes options).SPAdes 3.15.5 includes the following additional pipelines: If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use -isolate option. For such purposes you can use it at your own risk. SPAdes is not intended for larger genomes (e.g. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. Note, that SPAdes was initially designed for small genomes. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Version 3.15.5 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. You can also provide additional contigs that will be used as long reads. The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. The latest SPAdes paper describing various pipelines in a protocol format is available here. SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded from. This manual will help you to install and run SPAdes. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
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