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 as IRang...high throughput sequencing experiments, starting from the raw sequence reads,...1057 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 error rate. JumboDB is not a genome assembler by itself but rather a subroutine that translates a set of reads i...1053 days ago
Kmer: a suite of tools for DNA sequence analysis
More at https://help.rc.ufl.edu/doc/Kmer This also includes: A2Amapper: ATAC, Assembly to Assembly Comparision tool: Comparative mapping between two genome assemblies...1053 days ago
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1022 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotat...enome assembly together with annotation and visualization results from HTS raw reads....948 days ago
937 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 w...932 days ago
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Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are abl...dy levels, etc. Smudgeplots are computed from raw or even better from trimmed reads a...861 days ago