QuasR: Quantification and annotation of short reads in R
The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such a...hroughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alig...1053 days ago
JumboDB: tool for de Bruijn graph construction
jumboDB tool for fast de Bruijn graph construction from long sequences (reads or genomes) with very low err...lf but rather a subroutine that translates a set of reads into compressed de Bruijn gra...1049 days ago
1018 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mito...genome assembly together with annotation and visualization results from HTS raw reads. https://academic.oup.com/na...943 days ago
933 days ago
Peregrine & SHIMMER Genome Assembly Toolkit
Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from read...928 days ago
Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
This tool extracts heterozygous kmer pairs from kmer count databases and performs gym...idy levels, etc. Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype struct...857 days ago
829 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm fo...ased on the expected k-mer multiplicity in the reads, independently of the quality...t from Pacific Biosciences HiFi and continuous long reads or Oxford Nanopore reads, inc...819 days ago
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish in...PuffAligner requires considerably less memory to construct its index and align reads. PuffAligner strikes a desira...802 days ago