|400901||Mapping to Reference Genome Opensource|
Mapping of NGS reads to a reference genome using opensource tools (BWA, Bowtie). Output: SAM/BAM alignment file format. Price is based on 1 sample at 1/4 slide SOLID or equivalent of input data, with about 1-day delivery time.
|400902||SNP Calling Opensource|
SNP calling using SAMTools. Output: pileup format readable in Excel, with about 1-day delivery time *Free if mapping of NGS reads is done with AITbiotech.
|400903||Mapping to Reference Genome Bioscope|
Mapping of SOLiD reads to a reference genome using Bioscope's mapreads (ABI). Output: SAM/BAM alignment file format. Price is based on 1 sample at 1/4 slide SOLID or equivalent of input data, with about 3-day delivery time.
|400904||SNP Calling Bioscope|
SNP calling using diBayes. The diBayes package is the tool used to call Single Nucleotide Polymorphisms (SNPs) from mapped and processed SOLiD™ System color-space reads. Output: A list of SNPs; A consensus *.fasta file with the same number of bases as the reference sequence (optional); A list of all covered positions (optional). About 2-hr delivery time.
|400905||De Novo Assembly of NGS Reads *|
* For assembly of microbial genomes only. Use of velvet to do de novo assembly of SOLiD reads. Use of Oases to do de novo assembly of transcriptome reads. About 2-day delivery time Note: De novo assembly requires excellent coverage and good quality reads from the pure single host sample. Even if the above is fulfilled, the assembler may still produce contigs of small length or no contigs at all. As such, we cannot guarantee the success of the de novo assembly.
|400906||Copy Number Variation Analysis (Human)|
Human Copy Number Variation (CNV) tool detects Human CNV in SOLiD™ Human CNV tool system data that originates from a single human sample. Slide(s) from this sample description must be mapped to the hg18 reference to facilitate correct normalization. Output: Excel compatible *.out and *.gff files.
Look for inversions in SOLiD™ mate-pair data using ABI's Inversion tool. Output: Excel compatible Inversion *.gff file.
|400908||Large Indels Analysis|
Look for large indels in SOLiD™ paired-end or mate-pair data using ABI's Large Indel tool. Output:Excel compatible large-indels.gff file. The Large Indel tool works with either paired-end fragments or mate-pair clones to find sets of locus-spanning pairs with significantly deviated insert sizes compared to the average insert size of the entire library.