Quick start

SPAdes is an assembler for second-generation sequencing data (Illumina or IonTorrent). PacBio and Nanopore reads are supported only as supplementary data. SPAdes can assemble genomes, metagenomes, transcriptomes, viral genomes etc.

Download SPAdes binaries for Linux or MacOS. You can also compile SPAdes from source (requires g++ 9.0+, cmake 3.16+, zlib and libbz2). SPAdes requires only Python 3.8+ to be installed.
Test your SPAdes installation by running
```
    bin/spades.py --test
```

Useful one-liners

A single paired-end library (separate files, gzipped):

bin/spades.py -1 left.fastq.gz -2 right.fastq.gz -o output_folder

A single paired-end library (interlaced reads):

bin/spades.py --12 interlaced.fastq -o output_folder

Two paired-end libraries (separate files):

bin/spades.py --pe1-1 1_left.fastq --pe1-2 1_right.fastq \
              --pe2-1 2_left.fastq --pe2-2 2_right.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

Assemble a uniformly covered isolate bacterial genome :

bin/spades.py --isolate -1 left.fastq.gz -2 right.fastq.gz -o output_folder

Assemble a metagenome:

bin/spades.py --meta -1 left.fastq.gz -2 right.fastq.gz -o output_folder

Assemble a transcriptome:

bin/spades.py --rna -1 left.fastq.gz -2 right.fastq.gz -o output_folder

Assemble an RNA viral genome:

bin/spades.py --rnaviral -1 left.fastq.gz -2 right.fastq.gz -o output_folder

Available assembly modes

--isolate - converntional bacterial data;
--sc - single-cell bacterial data;
--meta - metagenome assembly;
--plasmid / --metaplasmid - plasmid discovery in conventional bacterial / metagenomic data;
--metaviral - viral assembly from metagenomic data;
--rna - transcriptome assembly (RNA-Seq);
--rnaviral - assembling viral RNA-Seq data;
--bio - assembly of non-ribosomal and polyketide gene clusters;
--corona - coronaviridae genome assembly;
--sewage - wastewater samples analysis.

Standalone SPAdes tools

spades-kmercount - k-mer counting;
spades-read-filter - read filtering using k-mer coverage;
spades-kmer-estimating - estimating number of unique k-mers;
spades-gbuilder - assembly graph construction;
spades-gsimplifier - assembly graph simplification;
spalgner - alignment of long reads to assembly graph;
spades-gmapper - specific alignment of long reads to assembly graph used in hybrid assembly pipeline;
binspreader - refinement of metagenome-assembled genomes.