blini

Blini

Lightweight nucleotide sequence searching and dereplication.

Requirements

None. Download and get started!

Usage

Searching

With both -q and -r set, Blini looks up the query entries in the reference entries. The reference may either be a fasta or a pre-sketched index.

blini -q query.fasta -r reference.fasta -o output.csv
# Or
blini -q query.fasta -r reference.blini -o output.csv

Sketching

With only -r set, Blini pre-sketches the given reference for use in search operations. This makes lookup operations quicker.

blini -r reference.fasta -o reference.blini

Clustering

With only -q set, Blini dereplicates (clusters) the query set.

blini -q input.fasta -o output_prefix

The outputs are a fasta file with the representatives, and a JSON file with the cluster assignments.

Other options

• -h display help on the available flags.
• -c for searching, calculate containment of query in the reference rather than full match.
• -m for searching and clustering, minimal similarity for a match.
• -s scale; use 1/s of kmers for similarity.

Limitations

• Blini supports nucleotide sequences only. Amino-acids are currently not supported.
• Blini runs on a single file with sequences, where each sequence is a separate species. Support for multiple files and multiple sequences per species will be added in the future.
• No multi-threading at the moment. Still fast, innit?