NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and gene...2114 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...n R, enter citation("PureCN")): Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using...2111 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...2040 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide poten...2040 days ago
1981 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
...ole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomi...1963 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...e construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...ontigs. Chimeric contig correction GFF lift-over Structural variant calling with and integrated version o...1860 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
...r that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene-calling algorithm and assigns putativ...1831 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1761 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...e construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes. Intact ord...of contigs. Misassembly correction GFF lift-over Structural variant calling with and integrated version o...1667 days ago