Split K-mer Analysis (version 2)

Description

This is a reimplementation of the SKA package in the rust language, by Johanna von Wachsmann, Simon Harris and John Lees. We are also grateful to have received user contributions from:

• Romain Derelle
• Tommi Maklin
• Joel Hellewell
• Timothy Russell
• Nicholas Croucher
• Dan Lu

Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses.

SKA can only align SNPs further than the k-mer length apart, and does not use a gap penalty approach or give alignment scores. But the advantages are speed and flexibility, particularly the ability to run on a reference-free manner (i.e. including accessory genome variation) on both assemblies and reads.

Documentation

Can be found at https://docs.rs/ska. We also have some tutorials available:

• From genomes to trees.

Installation

Choose from:

1. Download a binary from the releases.
2. Use cargo install ska or cargo add ska.
3. Use conda install -c bioconda ska2 (note the two!).
4. Build from source

For 2) or 4) you must have the rust toolchain installed.

OS X users

If you have an M1/M2 (arm64) Mac, we aren't currently automatically building binaries, so would recommend either option 2) or 4) for best performance.

If you get a message saying the binary isn't signed by Apple and can't be run, use the following command to bypass this:

xattr -d "com.apple.quarantine" ./ska

Build from source

1. Clone the repository with git clone.
2. Run cargo install --path . or RUSTFLAGS="-C target-cpu=native" cargo install --path . to optimise for your machine.

Differences from SKA1

Optimisations include:

• Integer DNA encoding, optimised parsing from FASTA/FASTQ.
• Faster dictionaries.
• Full parallelisation of build phase.
• Smaller, standardised input/output files. Faster to save/load.
• Reduced memory footprint and increased speed with read filtering.

And other improvements:

• IUPAC uncertainty codes for multiple copy split k-mers.
• Uncertainty with self-reverse-complement split k-mers (palindromes).
• Fully dynamic files (merge, delete samples).
• Native VCF output for map.
• Support for known strand sequence (e.g. RNA viruses).
• Stream to STDOUT, or file with -o.
• Simpler command line combining ska fasta, ska fastq, ska alleles and ska merge into the new ska build.
• Option for single commands to run ska align or ska map.
• New coverage model for filtering FASTQ files with ska cov.
• Logging.
• CI testing.

All of which make ska.rust run faster and with smaller file size and memory footprint than the original.

Planned features

• Sparse data structure which will reduce space and make parallelisation more efficient. Issue #47.
• 'fastcall' mode. Issue #52.

Feature ideas (not definitely planned)

• Add support for ambiguity in VCF output (ska map). Issue #5.
• Non-serial loading of .skf files (for when they are very large). Issue #22.
• Alternative mixture models for read error correction. Issue #50.

Things you can no longer do

• Use k > 63 (shouldn't be necessary? Let us know if you need this and why).
• ska annotate (use bedtools).
• ska compare, ska humanise, ska info or ska summary (replaced by ska nk --full-info).
• ska unique (you can parse ska nk --full-info if you want this functionality, but we didn't think it's used much).
• ska type (use PopPUNK instead of MLST 🙂)
• Ns are always skipped, and will not be found in any split k-mers.
• .skf files are not backwards compatible with version 1.