PATCH - Collection of software solutions for pangenome analyses
The PATCH (Pangenome Analysis Toolbox) is a comprehensive collection of software tools designed to facilitate pangenome analyses. The toolbox offers a range of command-line tools and web-based interfaces that enable researchers to analyze, compare, and predict the properties of multiple genomes.
Key Features:
- A suite of freely available command-line tools for phylogenetic reconstruction, local alignment search, core genome detection, and pangenome prediction
- Web-based interfaces for benchmarking and comparing tool performance
- Standardized interface (SOCKS) for colored k-mer sets to enhance comparability and interoperability between tools
Benefits:
- Facilitates efficient analysis of multiple genomes in parallel
- Enables researchers to predict the openness of a pangenome and estimate core genome size
- Enhances the comparability and interoperability of software tools in computational pangenomics
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SANSSANS is a freely available command line tool for phylogenetic reconstruction. It is alignment- and reference-free, and accepts (multiple) FASTA or FASTQ files containing complete genomes, assembled contigs, or raw reads as input. Sequence segments (in terms of k-mers) that are shared by a set of genomes are used as indicators for phylogenetic splits. Splits are combined, weighted, filtered and output in tab separated format. They can be visualized as a phylogenetic tree or network using existing tools such as SplitsTree. SANS is implemented in C++, and converter scripts for newick and nexus are provided. |
PLASTPLAST is a freely available command line tool enabling the heuristic search for highest scoring local alignments between a nucleotide sequence query and a graphical pangenome consisting of thousands of individual genomes. Input pangenomes may be given either as an existing sequence graph or as sets of (multiple) FASTA or FASTQ files containing complete genomes, assembled contigs, or raw sequencing reads. Highest scoring local alignments between a query and all sequences of the pangenome are searched based on a seed-and-extend approach. Alignment outputs may be enriched with information about the individual genomes whose sequences are involved in an alignment. A search may be restricted to specific parts a the pangenome with respect to sequence presence in certain individual genomes or with respect to their abundance among individual genomes. |
CorerCorer is a freely available command line tool enabling the detection of all genomic sequences forming the so-called core of a pangenome. An input pangenome is given as an existing sequence graph. Corer then computes its core genome, consisting of all k-length substrings occurring in at least q individual genomes and all short sequence fragments connecting them inside the graph. The q parameter and the maximum fragment length may be adjusted to compute either more conservative or more relaxed core genomes. Results may be outputted either as pure sequence fragments or as pruned versions of the input sequence graph. |
PangrowthPangrowth is a freely available command line tool designed to predict the |
PanBenchA major challenge in computational pangenomics is the memory- and time-efficient analysis of multiple genomes in parallel. Many software tools used in the current research follow the idea of colored k-mer sets to efficiently index and query a large collection of strings, but use different strategies when it comes to the implementation. The aim of this project is to evaluate the different solutions and establish a standard interface. The SOCKS interface (Software for colored k-mer sets) defines a common set of core features and standard input and output formats that software tools in computational pangenomics should implement. It aims to enhance the comparability and interoperability of these tools for the benefit of both developers and users. PanBench (Pangenomics Benchmark and Workbench) is an open catalog of software tools for computational pangenomics and is an example of what such a common interface makes possible. It allows users and developers to search for tools by different criteria, compare the performance of these tools, and test each tool in a user-friendly web interface before downloading and installing the software on their local machine. |