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@ -33,7 +33,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [MALT](#malt) - Sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics
- [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples for the same classifier/profiler.
- [TAXPASTA](#taxpasta) - Tool to standardise taxonomic profiles as well as merge profiles across samples for the same classifier/profiler.
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@ -445,7 +445,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
- `taxpasta`
- `<db_name>.<sample_id>*.{tsv,csv,arrow,parquet,biom}`: A list of taxonomic profiler output files. The standard format is the `tsv`. The first column describes the taxonomy ID and the rest of the columns describe the read counts for each sample.
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The following report files are used for the taxpasta step: