Hawkeye: an interactive visual analytics tool for genome assemblies
Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics too...2007 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a th...on of copy number variants (CNVs) from whole-exome sequencing data.EXCAVATOR has been publi...2004 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...nscripts from bulk and single-cell RNA-Seq data, or more generally o...et sequences using high-throughput sequencing reads. It is based on...nment. On benchmarks with standard RNA-Seq data, kallisto ...r, Near-optimal probabilistic RNA-seq quantification, Nature Biotechno...2001 days ago
2001 days ago
1997 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA u...to the reference with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to t...1987 days ago
1986 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 s...ecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between d...1977 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowi...ented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a refer...1959 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of o...using an EM algorithm Mining candidate STR alleles from population-scale sequencing data Employing a specialized...1942 days ago