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