GenomeMapper: Simultaneous alignment of short reads against multiple genomes
GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be u...2184 days ago
2181 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features...2149 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Cr...1993 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureC...2108 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as...2037 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing p...n. In such cases researchers often combine both technologies and the more erroneous long r...tter and more accurate integration of these two technologies. Results: We designed and dev...2096 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficul...2096 days ago
2095 days ago
LRCstats: a tool for evaluating long reads correction methods
LRCstats is an open-source pipeline for benchmarking DNA long r...an reads produced by next generation sequencing technologies, such as those produced by Il...t reads outputted by next generation sequencing technologies to correct long reads.2094 days ago