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Online documentation and access details to applications/software installed at ABCC

Showing 1 to 14 of 14


Next Generation Sequencing

ABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. First, the algorithm produces a draft assembly by concatenating different parts of raw reads. This coarse sequence is then polished into a high quality assembly.


Next Generation Sequencing

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.


Next Generation Sequencing

The basic goal of the pipeline is to take a large collection of reads generated from ChIP-seq or RNA-seq experiments associated with an individual and detect single nucleotide variants (SNVs) that correspond to significantly skewed number of reads.


Next Generation Sequencing

ALLPATHS-LG is an original short read assembler and it works on both small and large (mammalian size) genomes.


Next Generation Sequencing

AltAnalyze is an easy-to-use application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting.


Molecular modeling

Amber is a molecular dynamics software suite for carrying out molecular dynamics biomolecule simulations.


Next Generation Sequencing

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. Gene-based annotation. 2. Region-based annotations. 3. Filter-based annotation. 4. Other functionalities.


Visualization Tools

AnviÃââo is an analysis and visualization platform for ÃâËomics data.


Next Generation Sequencing

Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChipÃÂ arrays.


Next Generation Sequencing

The AQUAS pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (The AQUAS pipeline is based off the ENCODE (phase-3) transcription factor and histone ChIP-seq pipeline specifications (by Anshul Kundaje) in this google doc .


Next Generation Sequencing

Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.


Next Generation Sequencing

AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing.


Molecular modeling

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.


Molecular modeling

AutoDock-Vina is an automated receptor-ligand docking software.