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Agile sequence analysis

A suite of programs for analyzing massively parallel sequence data

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:

Fasta of fastq file manipulation

AgileQualityFilter

This program 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

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

AgileSamFileMerger

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

Autozygosity mapping with exome data

AgileGenotyper

This program 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. 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

This program 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

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

AgileVariantViewer

This program 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

This program 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

This program 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

This program reads unaligned reads in *.fastq and identifies somatic sequence variants occuring at specific genomic positions. AgileFastaVariantFinder page



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