1478 days ago
The wavefront alignment (WFA) algorithm
The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage ofhomologous region...ms that run in quadratic time, the WFA runs in time O(ns), proportional to the read lengt...1469 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for w...files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in B...1463 days ago
merqury: Evaluate genome assemblies with k-mers
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set c...1463 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, coverin...ique characteristics: Co-assembly procedure with read mapping for estimation of the...as. Metatranscriptomic support via mapping of cDNA reads agai...1419 days ago
1411 days ago
1348 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA wi...nt calling test with 30× coverage 2×150 reads, URMAP achieves high accurac...therefore pose an unrealistically easy challenge to read mappe...1345 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumina M...n on large datasets (10s of millions to billions of reads). An ITS-specific vers...verifiably removes primers on both ends of each ITS read, a ke...1333 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, an...sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Des...1294 days ago