SPAdes is a versatile toolkit for assembling and analysing sequencing data. It is primarily developed for Illumina sequencing data, can also be used with IonTorrent data, and most pipelines support hybrid assembly with supplementary long reads from PacBio and Oxford Nanopore.
The package provides multiple assembly pipelines together with supplementary tools for tasks related to sequencing data analysis and assembly processing.
This is free and open source software.
Key Features
- Provides assembly pipelines for isolates and single-cell bacterial data.
- Supports assembly of metagenomic data.
- Supports assembly of transcriptomic data.
- Supports hybrid assembly using supplementary long reads from PacBio and Oxford Nanopore.
- Includes modes to recover bacterial plasmids.
- Includes modes to recover RNA viruses.
- Provides HMM-guided assembly.
- Includes tools for efficient k-mer counting.
- Includes k-mer-based read filtering tools.
- Includes assembly graph construction and simplification tools.
- Includes sequence-to-graph alignment tools.
- Includes metagenomic binning refinement tools.
Website: github.com/ablab/spades
Support:
Developer: SPAdes team
License: GNU General Public License v2.0
SPAdes is written in C++. Learn C++ with our recommended free books and free tutorials.
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Read our verdict in the software roundup.
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