Bioinformatic Services

SeqWright's bioinformatics are designed to support our next-generation services by presenting the massive amounts of data generated by our SOLiD 3 plus and 454 Titanium platforms in an ordered and manageable form. Our bioinformatics services are highly customizable so we will work with you to generate files and reports which elucidate precisely the data you’re looking for. The following is a list of bioinformatic deliverables and capabilities for common next-gen applications:

Whole-genome de novo Sequencing:

SeqWright's whole-genome de novo sequencing services include draft sequence assembly. The completeness of the assembly depends on the size, content and complexity of the genome as well as the amount of sequencing coverage generated. Metrics such as quality scores for each base, number of scaffolds, number of contigs and the N50 number will be provided. Provided metrics can be further customized based on customer's requests. SeqWright does not currently provide annotation services for novel organisms. The following files will be provided with your de novo assembly:

Assembly summary with contig and scaffold metrics
Assembled scaffold
All contigs
Depth of coverage
Raw sequencing reads
Quality values

Whole-genome Resequencing:

SeqWright's whole-genome resequencing sequencing services include reference matching, SNP calling, copy number variation, Indels (small and large), quality scores, base coverage and SNP quality metrics. The following files will be provided with your resequenced genome:

Consensus sequence
Alignment report summarizing mapping results
SNP report including base change, coverage at SNP position, SNP type, affected gene and amino acid change (if applicable)
Raw sequencing reads with quality scores
Reads matching the genome including position & number of mismatches
Depth of coverage

Whole-transcriptome Sequencing:

SeqWright's whole-transcriptome sequencing services include counts for all known mRNAs, Heat maps, SNPs, novel transcribed regions with associated counts, novel splice variants and evidence of fusion genes. The following files will be provided with your whole-transcriptome results:

Raw sequencing reads and quality scores
Alignment report summarizing mapping results
Reads matching the genome including position & number of mismatches
Counts file containing the number of reads matching annotated exons
Coverage files allowing visualization in the UCSC genome browser
Optimization plots to aid novel transcribed region identification
Putative transcribed regions

Small RNA Profiling & Discovery:

SeqWright's small RNA profiling services include counts for all known small RNAs (under 40base pairs long) as well as counts for novel small RNAs. The following files will be provided with your de novo assembly:

Raw sequencing reads and quality scores
Alignment reports for matching to filter database, small RNA database and genome
Reads matching filter and small RNA databases including length and position of match
Reads matching the genome including length and position of match
Counts file including number of hits against filter and small RNA databases
Coverage files allowing visualization in the UCSC genome browser

Serial Analysis of Gene Expression (SAGE):

SeqWright's SAGE services provide an efficient means of comprehensive expression analysis with the capability to run multiple samples on a single slide. The following files will be provided with your SAGE project:

Raw sequencing reads
Mapping summary listing each tag, its frequency, its GenBank Identifier and a bried description of the identified gene
Reads matching the reference including their mapping positions and mismatches
File comparing tags in two different samples
File calculating the abundances of repeat reads

Learn more about the specifications for the various types of next-gen sequencing runs