Agile sequence analysis

A suite of programs for analyzing massively parallel sequence data

 

Agile variant viewer screenshot

AgileVariantViewer identifying a PXDN variant that causes congenital cataract, corneal opacity, and glaucoma (citation).

 

The Agile suite of programs allows the rapid analysis of clonal sequencing data, aligned to the human genome, with a view to identifying disease-causing sequence variants. Currently, the Agile suite consists of eight programs, each with its own user guide and download page, as described below:

Read quality filtering

AgileQualityFilter

AgileQualityFilter allows the filtering out of low quality sequences, with the exported data formatted as either FASTA or FASTQ. If the reads are 5′‑end tagged with sample identifiers, the program will also sort and remove the tags from the output data. AgileQualityFilter page

Sam file manipulation

AgileSamFileSorter

AgileSamFileSorter will sort the aligned sequence reads in an unordered SAM file by chromosome number and position. AgileSamFileSorter page

AgileSamFileMerger

AgileSamFileMerger combines two or more ordered SAM files to create a single ordered file. AgileSamFileMerger page

Autozygosity mapping with exome data

AgileGenotyper

AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data (see Genetic mapping). AgileGenotyper page

AgileVariantMapper

AgileVariantMapper visualises sequence variant data from whole exome data such that it is possible to identify autozygous regions in consanguineous individuals. The data can originate from files exported by AgileGenotyper, AgileAnnotator, AgileVariantViewer or a tab delimited text file formatted as described in the user guide webpage. AgileVariantMapper page

Germline mutation detection

AgileAnnotator

AgileAnnotator will read an ordered SAM file and identify any sequence variant present in a protein-coding exon or within 50 bp of a splice site. AgileAnnotator page

AgileKnownSNPFilter

AgileKnownSNPFilter will analyze sequence variants exported by AgileAnnotator and identify those previously found by the 1000 Genomes Project. AgileKnownSNPFilter page

AgileFileConverter

AgileFileConverter reformats data in tab delimited text files to a format that can be imported in to AgileVariantViewer or AgileFileViewer. Since many commercial NGS service provides supply variant data in tab delimited text files, AgileFileConverter allows this data to be analysed by the Agile suite of programs. AgileFileConverter page

AgileVariantViewer

AgileVariantViewer allows variants identified by AgileAnnotator and optionally filtered by AgileKnownSNPFilter to be visually filtered by read depth and by allele read depth ratio. AgileVariantViewer can then export sequence variants for the whole genome, single chromosome or chromosomal region. AgileVariantViewer page

AgileGeneFilter

AgileGeneFilter allows sequence variants exported from AgileVariantViewer to be filtered, by identifying the genes that contain them and then performing a textual data search on those genes using information downloaded from UniProt. AgileGeneFilter page

AgileFileViewer

AgileFileViewer reads a sequence variant file created by AgileAnnotator (or one filtered by either AgileKnownSNPFilter or AgileVariantViewer) and displays associated information for each variant. AgileFileViewer page

Somatic mutation detection

AgileFastaVariantFinder

AgileFastaVariantFinder identifies somatic sequence variants occuring at specific genomic positions and uses unaligned next generation sequence data. AgileFastaVariantFinderpage