The CGAT-apps code collection has been written over several years in the context of comparative genomics and more recently next-generation sequencing analysis.
The aim of the toolkit is to solve practical problems in the analysis of genomic data. The focus of the toolkit is to facilitate the interpretation of genomic data in a biological context. Furthermore, as a training institution our aim is to write code that is well structured and can serve as an introduction to advanced bioinformatic scripting for biologists.
Other toolkits with similar functionality¶
The CGAT code collection extends, complements but also overlaps various other toolkits. As all toolkits, and ours, continue to evolve, this is a very dynamic relationship. For example, our workflows frequently use other toolkits, in particular bedtools and the UCSC tools, for high-performance computations. Usage of common genomic file formats and a command line interface ensures compatibility.
Below is a list of toolkits with similar or complementarity functionality to the CGAT code collection and quotes from their respective web-sites:
bedtools The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by “streaming” several BEDTools together.
samtools SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
EMBOSS EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
GROK GROK (Genomic Region Operation Toolkit) is “Swiss Army knife” library for processing genomic interval data. GROK operates on genomic regions, annotated chromosomal intervals that represent sequencing short reads, gene locations, ChIP-seq peaks or other genomic features. Applications of GROK include file format conversions, set operations, overlap queries, and filtering and transformation operations. Supported file formats include BAM/SAM, BED, BedGraph, CSV, FASTQ, GFF/GTF, VCF and Wiggle.
biopieces The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.
fastx-toolkit The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.