TAXPASTA: TAXonomic Profile Aggregation and STAndardisation

Abstract

Metagenomic analysis is largely concerned with untargeted genetic characterisation of the taxonomic and functional composition of whole communities of organisms. Researchers ask questions from metagenomic sequencing such as 'who is present' (what organisms are present), and 'what are they doing' (which functions are they performing)? The nature of this field is such that it intersects with ecology, medicine, statistics, and bioinformatics. Facilitated by the development of Next-Generation Sequencing (NGS), the field often generates large datasets consisting of many samples (hundreds) and many sequencing reads (tens of millions).In part, due to the interdisciplinary nature of the field, but more importantly, due to the lack of a gold standard, the task of accurately identifying the taxonomic origin of each sequencing read is a popular and unresolved bioinformatics problem. Furthermore, the sizes of the datasets present interesting challenges for computational efficiency, which may require trading off accuracy for speed and memory use. Thus, there exists a diverse number of bioinformatics tools in order to analyse metagenomic sequencing data and produce metagenomic profiles. However, most of those tools have invented their own (often tabular) result formats, which complicates downstream analysis and in particular comparison across tools.TAXPASTA is a standalone command-line tool written in Python (Van Rossum & Drake Jr, 1995) that aims to standardise the diverse range of metagenomic profiler output formats to simple tabular formats that are readily consumed in downstream applications. TAXPASTA facilitates cross-comparison between taxonomic profiling tools without the need for external or dedicated modules or plugins needed of other 'dedicated' metagenomic profile formats.

A proposed workflow to analyze bacterial transcripts in RNAseq from blood extracellular vesicles of people with Multiple Sclerosis

“…Specific settings for each profiler were as follows: for kaiju , e-value=0.0001 and minimum-length=41; for kraken2 , confidence=0.90; for krakenuniq , hll-precision=16; and for centrifuge , minimum-hitlen=41. After the individual profiles were created, taxpasta v0.3.0 was used to standardize the outputs of the individual profilers into a common format [18]. The lines of the taxa were cut to genus level.…”

Acanthophis: a comprehensive plant hologenomics pipeline

“…Acanthophis can utilise any of Kraken 2 (Wood et al, 2019), Bracken (Lu et al, 2017), Kaiju (Menzel et al, 2016), Centrifuge (Kim et al, 2016), and Diamond (Buchfink et al, 2021) to create taxonomic profiles for each sample against any number of taxon identification databases; most tools supply pre-computed indices for public databases. Acanthophis can then optionally use taxpasta (Beber et al, 2023) to merge multiple profiles into a single combined table for easy downstream use.…”

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

“…Post-processing of taxonomic profiles include standardisation and aggregation of profiles , i.e. merging of multiple profiles into a single multi-sample table for easier comparison between profilers, with the tool TAXPASTA (Beber et al 2023), and visualisation of profiles with Krona (Ondov, Bergman, and Phillippy 2011) where supported.…”

“…One of the challenges that researchers face when comparing multiple taxonomic classifiers or profilers is the heterogenous output formats that are produced, that often require custom parsing and merging scripts for each tool to standardise. To facilitate more user-friendly cross-comparisons between tools, nf-core/taxprofiler utilises the TAXPASTA tool (Beber et al 2023) to generate standardised profiles and generate multi-sample tables.…”

“…For output, nf-core/taxprofiler, StaG-mwc, and sunbeam (via an extension) support a singular run report for summarising all preprocessing step. Only nf-core/taxprofiler and TAMA produce standardised output for all taxonomic profilers, the former with the dedicated standalone tool TAXPASTA (Beber et al 2023). However Unipro UGENE additionally offers a 'consensus' profile using WEVOTE (Metwally et al 2016).…”