Atlas2 is a next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data.
Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.
For each gap in a genome assembly, ATLAS GapFill identifies gap-associated sequence reads, performs local sequence assembly of the data and fills that gap with the newly assembled sequence contig.
SNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calls in an efficient way.
Atlas Whole Genome Assembly Suite
A suite of software tools for the assembly of large genomes.
Atlas Visualization Tools
Visualization tools in support of large-scale assembly.
MegaDot—A large-scale dot plotter
bcm-ace-plots—A tool to display contig template coverage, read coverage, quality, and high quality discrepencies
atlas-readpainter—A multiple alignment to reference tool
BCM Trace Viewer
BCM Java Alignment Viewer
PASH comparison method
An efficient large-scale sequence comparison method that uses positional hashing.
SimPed quickly generates haplotype and/or genotype data for pedigrees.
Solid-genotyper is a SNP discovery and genotyping tool for high coverage SOLiD data. This tool combines a logistics regression model and heuristics methods to characterize systematic sequencing error and overcome mapping bias issue.