Tool reference

This page summarizes prominent tools within the CGAT Code collection. The tools are grouped losely by functionality.

Genomic intervals/features

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Compute overlap statistics of multiple bed files.

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Transform interval data in a bed formatted file into a fasta formatted file of sequence data.

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Convert between interval data. Convert a bed formatted file to a gff or gtf formatted file.

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Work on gff formatted files with genomic features. This tools sorts/renames feature files, reconciles chromosome names, and more.

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Filter or merge interval data in a bed formatted file.

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Compare two sets of genomic intervals and output a list of overlapping features.

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Compute summary statistics of genomic intervals.

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Annotate genomic intervals (composition, peak location, overlap, ...)

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Decompose multiple sets of genomic intervals into various intersections and unions.

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Compare multiple sets of interval data sets. The tools computes all-vs-all pairwise overlap summaries. Permits incremental updates of similarity table.

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Convert between formats

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Split a file in gff format into smaller files. The script ensures that overlapping intervals remain in the same file.

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This script computes the genomic coverage of intervals in a gff formatted file. The coverage is computed per feature.

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Output genomic sequences from intervals.

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Compute distributions of interval sizes, intersegmental distances and interval ovelap from list of intervals.

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Summarize features within a gff formatted file.

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Convert between formats.

Gene sets

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Translate a gene set into genomic annotations such as introns, intergenic regions, regulatory domains, etc.

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Annotate transcripts in a gtf formatted file. Annotations can be in reference to a second gene set (fragments, extensions), aligned reads (coverage, intron overrun, ...) or densities.

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Annotate each base in the genome according to its use within a transcript. Outputs lists of junctions.

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Derive genomic intervals (intergenic regions, introns) from a gene set.

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merge exons/transcripts/genes, filter transcripts/genes, rename transcripts/genes, ...

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convert gene set in gtf format to tabular format.

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Compare two gene sets - output common and unique lists of genes.

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Compare multiple gene sets. The tools computes all-vs-all pairwise overlap of exons, bases and genes. Permits incremental updates of similarity table.

Sequence data

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Interleave paired reads from two fastq files into a single fasta file.

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Build an index for a fasta file. Pre-requisite for many CGAT tools.

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Count kmer content in a set of fasta sequences.

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Compute features of sequences in fasta formatted files

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Compare two sets of sequences. Outputs missing, identical and fragmented sequences.

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Segment sequences based on G+C content, gaps, ...

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Concatentate sequences from multiple files.

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In-silico creation of variants of protein coding sequences.

NGS data

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Compute meta-gene profiles from aligned reads in a bam formatted file. Also accepts bed or bigwig formatted files.

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Operate on bam formatted files - filtering, stripping, setting flags.

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Convert bam formatted file of genomic alignments into genomic intervals. Permits merging of paired read data and filtering by insert-size.

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Save sequence and quality information from a bam formatted file.

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Compute read densities over a collection of intervals. Also accepts bed or bigwig formatted files.

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Compute summary statistics of a bam formatted file.

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Convert read coverage in a bam formatted file into a wiggle or bigwig formatted file.

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Compute stats on exon over-/underrun and spliced reads.

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Compute coverage of reads within multiple interval types.

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Outputs side-by-side comparison of residue level counts between multiple bam formatted files.

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Perform quality score conversion between fastq formatted files.

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Interleave paired end data.

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Output bases below quality threshold, number of N’s, quality score distribution.

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Ensure that paired read fastq formatted files are consistent after filtering on the individual files.

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Perform read-by-read comparison of two bam-files.

Variants

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Sort a vcf file.

Genomics

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How many residues to the same locations, do different locations, etc.

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Output coverage statistics for a UCSC liftover chain file.