Next generation Sequence Analysis

Next-Gen Genomics has arrived and it has changed the way the research community is looking at diseases, genetic makeup and the genome. Ocimum Biosolutions now offers Next-Gen Data Analysis on all popular Next-Gen Sequencing platforms such as Roche 454, Illumina Solexa, ABI SOLiD™.

Whole genome and targeted resequencing

Whole genome resequencing allows characterization of genomes in terms of single nucleotide variations, insertions, deletions, copy number variations and other chromosomal rearrangements (inversions and translocations) in a single run. We carry out alignments or mapping of read sequences with known reference sequences. The mapping results are given in SAM/BAM format, which makes visualization and further processing easy. For variation analysis, we use proprietary and open source software. Results can be suppled in any standard specified format.

As the name itself indicates, the process involves sequencing of targeted regions. Many studies focus on some genes or specific regions, which require efficient methods to enrich these regions. Data analysis and tools will be same as whole genome resequencing.

Transcriptome analysis

Transcriptome analysis by sequencing (RNA-seq) has been recently developed that uses ultra high throughput sequencing technologies. Sequencing based methods are hypothesis neutral that allow to study both known and unknown transcripts, and enable to detect:

• expression of all coding and non-coding RNAs
• alternative splice events
• expressed SNPs or mutations
• fusion transcripts
• novel transcribed regions

Data analysis starts with mapping short reads to genomic reference and splice junctions. Counts of these mapped reads gene wise or exon wise can be used for digital gene expression analysis. Split mapping allows to find novel splice junctions.

e provide mapped results in SAM/BAM format and other application specific results will be given in simple text files in any specified format (GFF, BED, etc.)

Small RNA analysis

Small RNA consists many classes such as miRNA, siRNA, piRNA, rasiRNA and other uncharacterized classes. Sequencing based approach to study these small RNAs is hypothesis-neutral and enables profiling and discovery of these in a single run.

Data analysis starts with read mapping on to their pre-cursor sequences (miRBase sequences in case of micro RNA). Count of reads that are mapped to pre-cursor sequences will be given in GFF format. Further, unmapped reads are mapped to genomic reference and classified into piRNA, rasiRNA, snoRNA, unknown, and others based their origin. Finally, unknown mapped reads are processed to find novel small RNAs.

We provide mapped results in SAM/BAM format and other application specific results will be given in simple text files in any specified format.

ChIP-seq
Chromatin immunoprecipitation is a technique to find elements that are involved in protein-DNA interactions. Data analysis starts with mapping sample and control (optional, but recommended) read sequences to reference genome. Sample read sequences are from enriched peak regions (where proteins bound to DNA). Peak regions are identified based on these mapping results.

Identified peak regions are provided in GFF format and mapping results will be given in SAM/BAM format.

De novo assembly

The initial generation sequence of any organism is called de novo sequencing. We provide de novo draft assemblies from short reads. We will provide all assembled contigs or scaffolds in standard fasta format, quality reports on assembly, and read coverage for each contig or scaffold (reads are mapped back to assembled contig).

Metgenomics analysis

Metagenomics is the study of microbial flora from a common habitat. The goal of a metagenomics study is to understand the extent and role of microbial diversity. Initially, we carry out alignments of sequenced reads from the metagenomic sample against a database of known microbial sequences. Details of alignments for each read are captured in a database or spreadsheet. Further, aligned reads are processed to give taxonomical content of the sample. We use NCBI taxonomy to group/classify aligned reads. Deliverables are details about alignments provided in a database or spreadsheet, taxonomical content in a spreadsheet and a summary report.

DNA methylation analysis

DNA methylation is one of the epigenetic modifications, which plays essential role in physiology and disease processes. DNA methylation profiling can be done in enzymatic, chemical (biosulfite conversion), and enrichment methods. We support analysis for these methods. We carry out alignments of sequenced reads and alignment results are provided in SAM/BAM or GFF format, which can be easily visualized on integrative genomics viewer or UCSC genome browser. Other application specific results and summary reports are provided in specific text formats.