- Assembly of second-generation sequencing data (Illumina or IonTorrent);
- PacBio and Nanopore reads that are used as supplementary data only.
bin/spades.py --test
- A single paired-end library (separate files, gzipped):
bin/spades.py -1 left.fastq.gz -2 right.fastq.gz -o output_folder
- IonTorrent data:
bin/spades.py --iontorrent -s it_reads.fastq -o output_folder
- A paired-end library coupled with long PacBio reads:
bin/spades.py -1 left.fastq.gz -2 right.fastq.gz --pacbio pb.fastq -o output_folder
- Available assembly modes: --isolate , --sc , --plasmid , --meta , --metaplasmid , --metaviral , --rna , --rnaviral , --bio , --corona , --sewage .
- Standalone tools in SPAdes package: k-mer counting, k-mer cardinality estimation, k-mer-based read filtering, assembly graph construction, assembly graph simplification, alignment of long reads to an assembly graph, refinement of metagenomic binning.
Citation
If you use SPAdes in your research, please cite our latest paper.
In case you perform hybrid assembly using PacBio or Nanopore reads, you may also cite Antipov et al., 2015. If you use multiple paired-end and/or mate-pair libraries you may additionally cite papers describing SPAdes repeat resolution algorithms Prjibelski et al., 2014 and Vasilinetc et al., 2015.
If you use other pipelines, please cite the following papers:
- metaSPAdes: Nurk et al., 2017.
- plasmidSPAdes: Antipov et al., 2016.
- metaplasmidSPAdes / plasmidVerify: Antipov et al., 2019
- metaviralSPAdes / viralVerify: Antipov et al., 2020
- rnaSPAdes: Bushmanova et al., 2019.
- biosyntheticSPAdes: Meleshko et al., 2019.
- coronaSPAdes: Meleshko et al., 2022.
You may also include older papers Nurk, Bankevich et al., 2013 or Bankevich, Nurk et al., 2012, especially if you assemble single-cell data.
Feedback and bug reports
Please, leave your comments and bug reports at our GitHub repository tracker. If you have any troubles running SPAdes, please attach params.txt and spades.log from the output folder.
