BCM-HGSC Software
BCM-HGSC Software
Atlas2
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
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.
Go to Atlas-Link product page.
ATLAS GapFill
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.
Go to ATLAS Gapfill product page.
SNPTools
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.
Go to Atlas Whole Genome Assembly Suite product page.
Atlas Visualization Tools
Visualization tools in support of large-scale assembly.
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MegaDot—A large-scale dot plotter
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bcm-ace-plots—A tool to display contig template coverage, read coverage, quality, and high quality discrepencies
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atlas-readpainter—A multiple alignment to reference tool
Bang
A fast, easy to use, repeat suppressing search tool.
CBT++
A collection of C++ classes to aid the development of computational biology applications.
BCM Trace Viewer
A Java application/applet to display .scf traces and phred quality values.
Go to BCM Trace Viewer product page.
BCM Java Alignment Viewer
A Java application/applet to view sequence alignment files.
Go to BCM Java Alignment Viewer product page.
PASH comparison method
An efficient large-scale sequence comparison method that uses positional hashing.
Go to PASH comparison product page.
SimPed
SimPed quickly generates haplotype and/or genotype data for pedigrees.
Solid-genotyper
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.