JCVI: Research / Software
 
 
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Sequencing/Assembly

AMOS

Manipulation of input and output files related to whole-genome shotgun assembly. Currently maintained at CBCB at the University of Maryland.

CABOG

CABOG assembles long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.

DNA Barcode Deconvolution

This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid.

Elvira

High throughput assembly of amplicon reads for virus-sized genomes.

JCVI Primer Designer

High throughput PCR primer design software.

Jillion

Java framework for reading, writing, analyzing and manipulating sequence and assembly data. Jillion supports most common data file formats...

Lucy

A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses.

TIGR Assembler

Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003.

TIGR SSS

Middleware for organizing large chunks of data to free the client from having to encode data storage specifics.

Gene Finding

Glimmer

A microbial gene-finding system, especially in bacteria, archaea, and viruses. Currently maintained at CBCB at the University of Maryland.

Annotation

AAT

A tool for analyzing and annotating eukaryotic genomic sequences.

JCVI Prokaryotic Annotation Pipeline

The automated Prokaryotic Annotation Pipeline was developed to generate on demand ORF prediction and functional annotation for prokaryotic...

Manatee

Web-based gene evaluation and genome annotation tool to view, modify, and store annotation for prokaryotic and eukaryotic genomes.

PASA

A eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene...

PROVEAN

A tool for predicting if an amino acid substitution and small indel affects protein function based on sequence alignment scores.

SIFT

A tool for predicting if an amino acid substitution affects protein function based on the degree of conservation of amino acid residues.

VariantClassifier

A Hierarchical Variant Classifier for Annotated Genomes

VIGOR

VIGOR (Viral Genome ORF Reader) is a web application tool to predict protein sequences encoded in small viral genomes. It determines the...

Genome Analysis

ANDES Tools

Statistical tools for the analysis of deep sequencing.

Cloe

Cloe is a contig visualization and finishing editor written in Java.

DAGchainer

The DAGchainer software computes chains of syntenic genes found within complete genome sequences.

k-mer Tools

DNA sequence analysis tools including ESTmapper, Snapper (for mapping reads), and ATAC (for aligning genomes).

MUMmer

MUMmer is a system for rapidly aligning entire genomes (draft or complete). Currently maintained at CBCB at the University of Maryland.

PanOTC

PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species...

PhageFinder

A tool to identify prophage regions within bacterial genomes.

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Metagenomics Analysis

Corbata: CORE MicroBiome Analysis Tools

Corbata is used to analyze the core members across the microbiome of a group of samples (cohort).

Metarep

An open source suite of tools for high-performance comparative metagenomics.

O-META

O-META (Ontologies based metadata tracking system) is a data driven application that can be configured to track project, study, sample,...

Microarray Tools

Ginkgo

Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis and normalization package.

Magnolia

Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays.

SNP Filter Scripts

Scripts to identify and filter out false positive SNP calls that are present in raw data from Affymetrix GeneChip® resequencing arrays.

TM4

TM4 is a suite of open source software tools that manage and analyze data from microarray experiments.

Proteomics Tools

APEX

The APEX tool is an implementation of the Absolute Protein Expression quantitation technique, computing protein abundance values for...

Cloud

JCVI Cloud BioLinux

Enabling scientists to quickly provision cloud-based bioinformatics platforms such as Amazon EC2 and Eucalyptus.