Variant identification software tools | Shotgun metagenomic sequencing data analysis
Although many tools are available to study variation and its impact in single genomes, there is a lack of algorithms for finding such variation in metagenomes. This hampers the interpretation of metagenomics sequencing datasets, which are increasingly acquired in research on the (human) microbiome, in environmental studies and in the study of processes in the production of foods and beverages.
Integrates workflow technology and in-built access to bioinformatics resources including remote data warehouses and tools. Galaxy permits users without programming skills to conduct computational analysis through the Web. It builds a succession of tools to perform multistep studies and is able to conserve the complete provenance of each analysis step. This platform offers drag and drop functionalities to ease the construction of workflows.
Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.
Analyses next generation sequencing (NGS) data. ANGSD can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. The tool is especially useful for low and medium depth data. The tool allows the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
Provides a reference-based single nucleotide variant (SNV) discovery and phylogenomic tree-building pipeline. SNVPhyl can analyse many genomes, identify variants and generate a maximum-likelihood phylogeny, an all-against-all SNV distance matrix. It is able to produce quality information to guide interpretation of the results. This tool differentiates outbreak isolates at low levels of contamination but cannot be used to evaluate the degree of contamination.
Allows definition and execution of bioinformatics pipelines. Bpipe was created in response to a need to frequently run many variations of a pipeline with stages deleted, inserted, reordered or adjusted. The software is implemented in, a language that supports creation of Domain-Specific Languages for the Java Virtual Machine, and it does not require knowledge of either language to implement pipelines. It includes features such as automatic connection of stages, audit trail or transactional management of tasks.