Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves bot...2070 days ago
vcfR: a package to manipulate and visualize VCF data in R
VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data i...2070 days ago
Referee: Genome assembly quality scores
Modern genome sequencing technologies provide a succint measure of quality at each po...embly. This allows for easy filtering of low quality sites for any downstream analysis. https://github.com/gwct/ref...2060 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence fil...from this SAMStat can be used to verify individual processing steps in large analysis pipelines....2055 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
ANItools is a software package written by PERL scripts that can be run in a Linux/Uni...ectly. Or you could send us the genome sequence by email. Then we will do the analysis work for you. https://academ...2051 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and enginee...2050 days ago
GWASpro: A High-Performance Genome-Wide Association Analysis Server
GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted...2027 days ago
SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
The software package SiLiX implements an ultra-efficient algorithm for the clust...lows the study of very large datasets. SiLiX is already included in the analysis pipeline for HOGENOM.2022 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in netwo...2021 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes con...n as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the...2018 days ago