Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to cluster...ters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide poten...2024 days ago
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 bo...2018 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...2018 days ago
1964 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequen...rogeneous hidden Markov model algorithm and a calling method that classifies genomi...ware package for the detection of copy number variants (CNVs) from whole-exome sequ...1947 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidizat...iploids, triploids and tetraploids, on the basis of frequency distributions at variant...1920 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...g of contigs. Chimeric contig correction GFF lift-over Structural variant calling with and integrated version o...1843 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a t...ed set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putativ...1815 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkena...1811 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1745 days ago