Accelerating spliced alignment of long RNA sequencing reads using parallel maximal exact match retrieval

A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.

De novo construction of isoforms from long-read data

Snakemake pipeline for benchmarking read mappers

WFA-lib: Wavefront alignment algorithm library v2

Visualizing transcript structure and annotation using ggplot2

A compressed, associative, exact, and weighted dictionary for k-mers.

Extremely fast non-cryptographic hash algorithm

a toolset for fast DNA read set matching and assembly using a new type of reduced kmer

A versatile toolkit for k-mers with taxonomic information

Experimental implementation of Cubical Type Theory

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

Efficient low-divergence mapping of long reads in minimizer space

The complete sequence of a human genome

Code examples of fast and simple k-mer counters for tutorial purposes

A very fast hashtable

A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)

An c++ implemention of strobemer

A tool for de novo clustering of long transcriptomic reads

Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array

A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.

This is the development home of the workflow management system Snakemake. For general information, see

A tool to identify, orient, trim and rescue full length cDNA reads

Sequence-to-graph mapper and graph generator

Developments in next generation sequencing: instruments, read lengths, throughput. See

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

SIMD partial order alignment tool/library

A console-based alignment viewer