-
Notifications
You must be signed in to change notification settings - Fork 0
Home
oxli is a powerful Rust library with a simple Python interface for counting k-mers in genomic sequencing data.
Use oxli to bring fast kmer counting and comparison operations to your Python projects!
This library is written on top of the sourmash rust library, and the underlying code for dealing with sequence data is well tested and maintained.
Authors: C. Titus Brown (@ctb), ctbrown@ucdavis.edu Adam Taranto (@adamtaranto)
Installing Oxli
Basic Setup
For Developers
Getting Started
Getting Started
Counting Kmers
Basic Counting
Extracting from Files
Handling Bad Kmers
Looking up Counts
Single Kmer Lookup
Multiple Kmer Lookup
Removing Records Remove Kmers Abundance Filtering
Exploring Count Tables
Iterating Records
Attributes
Set Operations
Basic SetOps
Exporting Data
Histo: Export Frequency Counts
Dump: Write Hash:Count Pairs
Save and Load KmerCountTables