This page serves as an index for the applications written and distributed by the Yandell, Marth, and Quinlan labs. Each item may include links to: documentation, code, and publications.
Software is listed with most recent releases first.
VARPRISM (VARiant PRIoritization SuM)
Variant Prioritization
A software package that identifies genes with a statistical excess of damaging de novo mutations among individuals with a genetic disease. VARPRISM incorporates functional variant prediction information (the VAAST CASM score) to improve the statistical power of risk gene mapping and controls for local mutation rate heterogeneity. The beta version of VARPRISM is currently available for download.
VCFAnno
Variant Annotation
Annotates a VCF with any number of sorted and tabixed input BED, BAM, and VCF files in parallel. It does this by finding overlaps as it streams over the data and applying user-defined operations on the overlapping annotations.
Taxonomer
Metagenomics
Yandell Lab,Marth Lab,Eilbeck Lab
Taxonomer is an ultrafast web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host mRNA transcript profiling.
RUFUS
Variant Calling
A new approach to variant detection that does not rely on mapping or whole genome assembly methods.
WHAM (WHole-genome Alignment Metrics)
Variant Calling
A structural variant (SV) caller that integrates several sources of mapping information to identify SVs. WHAM classifies SVs using a flexible and extendable machine-learning algorithm (random forest).
Genome Query Tools (GQT)
Data Management,Query Tools
A command line tool and a C API for storing and querying large-scale genotype data sets like those produced by 1000 Genomes, the Uk100K, and forthcoming datasets involving millions of genomes.
SpeedSeq
Variant Annotation,Variant Calling
An open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement.
Peddy
Pedigree Analysis
Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF.
MAKER-P
Genome Annotation
A pipeline designed to make the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and resources.
Iobio
Data Visualization
iobio uses immediate visual feedback to make understanding complex genomic datasets more intuitive, and analysis more interactive.
Poretools
A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.
BEDTools
Data Management
A swiss-army knife of tools for a wide-range of genomics analysis tasks. Intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely used genomic file formats such as BAM, BED, GFF, VCF.
Lumpy
Variant Calling
A probabilistic framework to integrate multiple structural variation signals such as discordant paired-end alignments and split-read alignments.
pVAAST (pedigree Variant Annotation, Analysis & Search Tool)
Pedigree Analysis
A disease-gene identification tool designed for high-throughput sequence data in pedigrees.
PHEVOR (Phenotype Driven Variant Ontological Re-ranking tool)
Phenotype Tools,Variant Prioritization
Integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles.
MOSAIK
A stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome.
GEMINI
Data Management,Query Tools
A powerful framework for exploring genetic variation in the context of the wealth of existing genome annotations that are available for the human genome.
GPAT ++ (Genotype Phenotype Association Toolkit)
Phenotype Tools
The application of population genomics to non-model organisms is greatly facilitated by the low cost of next generation sequencing (NGS).
ImagePlane
Data Visualization
Python based software for the automated analysis of images of the animal S. mediterranea. This software allows quantification and categorization of the animal's morphology.
VAAST 2 (Variant Annotation, Analysis & Search Tool)
Variant Prioritization
Probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences.
BamTools
Variant Calling
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
RepeatRunner
Genome Annotation
A CGL-based program that integrates RepeatMasker with BLASTX to provide a comprehensive means of identifying repetitive elements.
CGL (Comparitive Genomics Library, and pronounced as “Seagull”)
Provides an informatics infrastructure for a laboratory, department, or research institute engaged in the large-scale analysis of genomes and their annotations.
Scissors
A split-read aligner that maps orphaned read mates (i.e. where one end-mate is aligned with high mapping quality, but the other mate is unmapped), as well as re-maps severely clipped reads (reads mapped with many unaligned or “clipped-off” bases).