skani is a program for calculating average nucleotide identity (ANI) from microbial DNA sequences (contigs/MAGs/genomes) for ANI > ~80%.
skani uses an approximate mapping method without base-level alignment to get orthology in order to estimate ANI. It is magnitudes faster than BLAST based methods and almost as accurate. skani offers:
Accurate ANI calculations for MAGs. skani is accurate for incomplete and medium-quality metagenome-assembled genomes (MAGs). Sketching methods (e.g. Mash), which may underestimate ANI for incomplete MAGs.
Aligned fraction results. skani outputs the fraction of genome aligned, whereas sketching methods do not.
Fast computations. Indexing/sketching is ~ 3x faster than Mash, and querying is about 25x faster than FastANI (but slower than Mash).
Efficient database search. Querying a genome against a preprocessed database of >65000 prokaryotic genomes takes a few seconds with a single processor and ~6 GB of RAM. Constructing a database from genome sequences takes a few minutes to an hour.
We added new experiments on the revised version of our preprint (pending bioRxiv update) in the appendix. We show skani has quite good AF correlation with MUMmer, and that it works decently on simple eukaryotic MAGs, especially with the --slow option (see below).
--no-learned-ani.--fast and --slow mode added - alias for -c 200 and -c 30 respectively.Requirements: 1. rust programming language and associated tools such as cargo are required and assumed to be in PATH. 2. A c compiler (e.g. GCC) 3. make
Building takes a few minutes (depending on # of cores).
```sh git clone https://github.com/bluenote-1577/skani cd skani
cargo install --path . --root ~/.cargo skani dist refs/e.coli-EC590.fasta refs/e.coli-K12.fasta
```
We offer a pre-built statically compiled executable for x86-64 linux systems. That is, if you're on a x86-64 linux system, you can just download the binary and run it without installing anything.
For using the latest version of skani:
sh
wget https://github.com/bluenote-1577/skani/releases/download/latest/skani
chmod +x skani
./skani -h
Note: the binary is compiled with a different set of libraries (musl instead of glibc), possibly impacting performance (slightly). Probably not a huge deal.
See the Releases page for obtaining specific versions of skani.
sh
conda install -c bioconda skani
Note: I highly recommend options 1 and 2 over using conda right now. skani is being developed quickly. The conda version will always be outdated. I'll remove this message when I feel skani is more stable.
```sh
skani dist genome1.fa genome2.fa -t 5
skani dist -q query1.fa query2.fa -r reference1.fa reference2.fa -o all-to-all_results.txt
skani sketch genomestosearch/* -o database skani search query1.fa query2.fa ... -d database
skani dist database/query.fa.sketch database/ref.fa.sketch
skani triangle genomefolder/* > skaniani_matrix.txt
python scripts/clustermaptriangle.py skaniani_matrix.txt
```
For more information about using the specific skani subcommands, see the guide linked above.
See the advanced usage guide linked above for more information about topics such as:
If the resulting aligned fraction for the two genomes is < 15%, no output is given.
In practice, this means that only results with > ~82% ANI are reliably output (with default parameters). See the skani advanced usage guide for information on how to compare lower ANI genomes.
The default output for search and dist looks like
Ref_file Query_file ANI Align_fraction_ref Align_fraction_query Ref_name Query_name
refs/e.coli-EC590.fasta refs/e.coli-K12.fasta 99.39 93.95 93.37 NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence
- Reffile: the filename of the reference.
- Queryfile: the filename of the query.
- ANI: the ANI.
- Alignedfractionquery/reference: fraction of query/reference covered by alignments.
- Ref/Query_name: the id of the first record in the reference/query file.
Jim Shaw and Yun William Yu. Fast and robust metagenomic sequence comparison through sparse chaining with skani. bioRxiv (2023). https://doi.org/10.1101/2023.01.18.524587. Submitted.
skani is actively being developed by me (Jim Shaw). I'm more than happy to accommodate simple feature requests (different types of outputs, etc). Feel free to open an issue with your feature request on the github repository. If you catch any bugs, please open an issue or e-mail me (e-mail on my website).