Skip to content

SPAdes Specifications

Process Details

  • Name: SPAdes
  • Process UUID: 6dbkda5jt1ry53lmvddktxckguvqfa
  • Process Group: Assembly

Overview

SPAdes is a genome assembler designed for short-read sequencing data. This process performs de novo assembly of bacterial, metagenomic, RNA, viral, and plasmid sequences using the SPAdes v4.0.0 algorithm. The assembler can handle both single-cell and standard sequencing data, with specialized modes for different types of genomic material.

This process is implemented in Bash, which invokes the SPAdes assembler and Python scripts for assembly statistics calculation.

Key Functionality

  • De Novo Assembly: Constructs contigs from paired-end short reads using graph-based algorithms
  • Multi-Modal Assembly: Supports specialized assembly modes for metagenomes, bacterial cultures, RNA, viral sequences, and plasmids
  • Quality Control: Generates assembly statistics including contig counts, sizes, and length distributions
  • Output Processing: Produces FASTA files, assembly graphs, and optional statistical summaries

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Paired-end sequencing reads for assembly
    • Format: FASTQ

  • Mate

    • Description: Mate pair information for paired-end reads
    • Format: Mate file

Outputs

  • Fasta File

    • Description: Assembled contigs in FASTA format
    • Format: FASTA

  • Log File

    • Description: SPAdes assembly log containing process information and statistics
    • Format: LOG

  • CSV File

    • Description: Assembly statistics including contig counts, sizes, and length distributions
    • Format: CSV

  • Output File Txt

    • Description: Additional assembly output files and intermediate results
    • Format: TXT

  • Fasta

    • Description: Final assembled contigs file
    • Format: FASTA

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • SPAdes Optional Parameters

    • Description: Optional Parameters for SPAdes Short-Read Assembler
    • Default value: --only-assembler

  • Would you like the stats output?

    • Description: Choose 'Yes' if you'd like the stats for SPAdes assembly results
    • Available options: yes, no (default)

  • SPAdes assembly options

    • Description: Choose the assembly option you'd like to run
    • Available options: Metagenome, Bacterial (Culture), Bacterial (Meta), RNA, Viral (RNA), Viral (Meta), Only Assembly (default)

References & Resources

  • Tool Documentation: Contact the team for details on calc_ctg_lens.py
  • Related Papers: Bankevich, A., Nurk, S., Antipov, D., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455-477. DOI: 10.1089/cmb.2012.0021