Assemble metagenomic reads using the SPAdes assembler.
This is a KBase wrapper for the metaSPAdes genomic reads assembler. MetaSPAdes is designed for assembling shotgun metagenomic reads.
- Currently the wrapper only supports Illumina, IonTorrent, PacBIO CLR and PacBIO CCS in FASTQ format, either uncompressed or gzipped.
- The --careful flag is always used, except for metagenomic assemblies where it is not allowed.
- Metagenome and Plasmid assembly can only be run on one reads library.
- Metagenome assembly can only be run on a paired end library.
- Illumina and IonTorrent reads can not be mixed in the same assembly.
- PacBIO CLR needs to be run with at least one accompanying Illumina or IonTorrent library.
- The k-mer parameter is autodetected by SPAdes, if the values are not specified in input.
- The PHRED parameter is autodetected by ea-utils.
- metaSPAdes might be very sensitive to the presence of the technical sequences remaining in the data (most notably adapter sequence regions), hence the authors recommend that you run quality control and pre-process your data prior to assembly. KBase has multiple Apps such as Trimmomatic and Cutadapt that can be used for sequence cleaning.
For questions, please contact us.
SPAdes version: 3.15.3 was released under GPLv2 on July 22, 2021
- Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27:824 834. doi: 10.1101/gr.213959.116 , https://www.ncbi.nlm.nih.gov/pubmed/28298430
- Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes De Novo Assembler. Curr Protoc Bioinformatics. 2020 Jun;70(1):e102. doi: 10.1002/cpbi.102. , https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpbi.102
Module Commit: ee3f83f9d451a7d0ad86709e55e8653bee497e30