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short-read-assembly

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

When to use

• assembling a bacterial isolate
• assembling a fungal genome
• assembling a small-eukaryotic genome
• assembling a single-cell genome
• assembling a metagenome genome
• deciding if short reads can produce the assembly
• bacterial finishing
• hybrid Illumina+long-read assembly

When not to use

• assembling a large, repeat-rich, heterozygous eukaryote
• producing a finished genome
• reproducing old papers with superseded tools

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