1406 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA w...ome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy...1340 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...ugh workflow optimized to run on large datasets (10s of millions to billions of reads). An ITS-specific versi...1328 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 f...uence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (p...1289 days ago
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in sev...1285 days ago
FastProNGS: fast preprocessing of next-generation sequencing reads
FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.1283 days ago
CoverM: Read coverage calculator for metagenomics
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative...by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in vari...1158 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnz...1241 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721205 days ago
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes...ss, an approach that has been successful with short reads. https://academic.oup.com/ve...1104 days ago