Bioinformatics Services

The sheer volume of data generated using high-throughput sequencing creates many informatic challenges. We offer bioinformatics support associated with data management, read mapping, individual consultations, and extended analysis. We also can point you in the right direction with a variety of services.

Service Charge

CLC Genomics Workbench Software

CLC Genomics Workbench performs both de novo assembly and super-fast reference assembly on hybrid data (454, Heliscope, Illumina GA, SOLiD, Sanger) of any genome size. It has full support for bar coded data and full visualization of contigs with all NGS reads and their quality scores.

CLC Genomics Workbench supports amongst others also

• Detection of single nucleotide and indel polymorphisms.
• Mapping of whole transcriptome and tag-based sequencing reads, identification of putative exons, and expression analysis.
• ChIP-seq experiment analysis.

For more info: CLC Genomics Workbench Software

CLC Sequence Viewer Software - (Free)

A Sequence Viewer for basic bioinformatics.

For more info: CLC Sequence Viewer Software

Bowtie

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

For more info: http://bowtie-bio.sourceforge.net/

SAMtools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

• Is flexible enough to store all the alignment information generated by various alignment programs
• Is simple enough to be easily generated by alignment programs or converted from existing alignment formats
• Is compact in file size
• Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory
• Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

For more info: http://samtools.sourceforge.net/

TopHat

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

For more info: http://tophat.cbcb.umd.edu/

Cufflinks

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

For more info: http://cufflinks.cbcb.umd.edu/

GenomeView

GenomeView is a next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.

For more info: http://genomeview.org

QIIME

QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. QIIME can run on a laptop, a supercomputer, and systems in between such as multicore desktops. Linux and Mac OS X are supported natively, and Windows, Linux, and Mac OS X are supported via the QIIME virtual box.

For more info: http://qiime.org/

Velvet

Velvet is a de novo genomic assembler specially designed for taking in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

For more info: http://www.ebi.ac.uk/~zerbino/velvet/

Galaxy

Galaxy is a web-based tool that enables researchers to use NGS tools and create workflows in a web-based environment.

For more info: http://galaxyproject.org

Tufts Researchers can elect to have their sequence data deposited directly into the Tufts Galaxy Server.

GenomeQuest

With GenomeQuest, researchers can:

• Store and interactively analyze all their NGS run results online
• Compare and combine their results with sequence/annotation data from the world's largest collection of sequence reference databases
• Use standard workflows to perform discovery (ChIP-Seq, RNA-Seq (Including Junction Discovery), Whole Genome Analysis, Metagenomics, etc.)
• Configure these built-in workflows or create new workflows
• Share and aggregate their results with lab members and collaborators
• Interface with other popular tools and systems -- including visualization, pathway analysis, LIMs, etc.
• Read from all popular instruments, including Life, Illumina, Roche, and more
• Manage sequence data across all related projects.

Sign up for a Free Basic Account: http://www.genomequest.com

DNAnexus

Next-gen sequence analysis and visualization, researchers can:

• On-demand compute and storage infrastructure
• Access everything through your web browser
• Long-term data storage and instant sharing
• Interactive genomic visualization
• RNA-Seq, ChIP-Seq, tag-based analysis
• Sequence variation detection
• Illumina, SOLiD, and Complete Genomics support

Sign up for a Free Basic Account: https://dnanexus.com