alshai / r-index
An optimal space run-length Burrows-Wheeler transform full-text index
☆26Updated 3 years ago
Related projects ⓘ
Alternatives and complementary repositories for r-index
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆22Updated 2 weeks ago
- Lift-over alignments from variant-aware references☆34Updated last year
- ☆25Updated 3 years ago
- A long read simulator based on badread idea☆20Updated 2 years ago
- ☆28Updated last year
- Population-scale detection of novel sequence insertions☆27Updated 2 years ago
- Indel-aware consensus from aligned BAMs☆20Updated last year
- Extracts subgraphs or components from a graph in GFA format☆23Updated this week
- Utilities to detect and profile `het-kmers`☆11Updated 3 months ago
- Hidden Markov Model based Copy number caller☆20Updated last month
- convert variation graph alignments to coverage maps over nodes☆21Updated last week
- GFA insert into GenomicSQLite☆48Updated 3 years ago
- ☆16Updated 3 years ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Updated 7 months ago
- Toolkit for extracting SVs from long sequences and benchmarking variant callers☆13Updated 7 years ago
- Snakemake pipeline for benchmarking read mappers☆16Updated 11 months ago
- A simple tool to fix PacBio fasta/q that was not properly split into subreads☆14Updated 3 years ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated 6 months ago
- Rust wrapper for the next generation (still currently in C++)☆20Updated this week
- Classify sequencing reads using MinHash.☆48Updated 4 years ago
- recompute GFA link overlaps☆25Updated 2 years ago
- Align subreads to ccs reads☆13Updated last year
- Comprehensive alignment, whole-genome coverage, and capture coverage statistics.☆19Updated 2 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆34Updated last year
- ☆14Updated 4 years ago
- This repo is deprecated. Please use gfatools instead.☆16Updated 6 years ago
- A long-read analysis toolbox for cancer and population genomics☆20Updated 8 months ago