SPAdes

Overview

SPAdes (St. Petersburg genome Assembler) is a versatile de Bruijn graph-based assembler designed for small genomes such as bacteria, fungi, and other microorganisms. It uses multiple k-mer sizes to build and merge assembly graphs, which helps resolve repeats and low-coverage regions. SPAdes supports Illumina short reads, IonTorrent data, and hybrid assembly when long reads (PacBio or Nanopore) are available alongside short reads. The --careful mode runs an additional mismatch correction step that reduces errors in the final contigs.

Installation

mamba install -c bioconda spades

Basic Usage

Assemble a bacterial genome from paired-end Illumina reads using the careful mismatch correction mode.

# Bacterial genome assembly with short reads
spades.py -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz \
  -o spades_output/ --careful -t 8 -m 32

Hybrid assembly combining short reads with Nanopore long reads for improved contiguity.

# Hybrid assembly (short + long reads)
spades.py -1 short_R1.fastq.gz -2 short_R2.fastq.gz \
  --nanopore long_reads.fastq.gz \
  -o spades_hybrid/ -t 8

Key Parameters

Flag / option	Description
`-1` / `-2`	Input paired-end FASTQ files (read 1 and read 2).
`-s`	Input single-end / unpaired reads.
`--nanopore`	Nanopore long reads for hybrid assembly.
`--pacbio`	PacBio long reads for hybrid assembly.
`-o`	Output directory for all assembly results.
`--careful`	Run MismatchCorrector post-processing to reduce mismatches and short indels in the final contigs.
`-t`	Number of CPU threads (default 16).
`-m`	Memory limit in gigabytes (default 250).
`-k`	Comma-separated list of k-mer sizes (default auto-selected).
`--isolate`	Mode optimised for high-coverage isolate genomes.

Expected Output

SPAdes writes output to the specified directory:

contigs.fasta – assembled contigs in FASTA format.
scaffolds.fasta – scaffolded sequences produced from the contigs.
assembly_graph_with_scaffolds.gfa – the assembly graph in GFA format.
spades.log – detailed log of the assembly run with timing and parameter information.
K21/, K33/, K55/, … – intermediate assemblies for each k-mer size used.