spades

genome assembler for single-cell and isolates data sets

Description

The SPAdes – St. Petersburg genome assembler is intended for both standard isolates and single-cell MDA bacteria assemblies. It works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio and Sanger reads. You can also provide additional contigs that will be used as long reads.

This package provides the following additional pipelines:

* metaSPAdes – a pipeline for metagenomic data sets

* plasmidSPAdes – a pipeline for extracting and assembling plasmids

from WGS data sets

* metaplasmidSPAdes – a pipeline for extracting and assembling

plasmids from metagenomic data sets

* rnaSPAdes – a de novo transcriptome assembler from RNA-Seq data

* truSPAdes – a module for TruSeq barcode assembly

* biosyntheticSPAdes – a module for biosynthetic gene cluster

assembly with paired-end reads

SPAdes provides 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).

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Homepage

http://cab.spbu.ru/software/spades/

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