millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-25 08:09:54 +00:00
Code Issues Releases Packages Activity

Prettier for docs

Browse source
This commit is contained in:
sofstam 2023-02-16 16:38:00 +01:00
parent dad64a688d
commit c9b521234b
1 changed files with 2 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

4
docs/output.md
View file

@ -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 - [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 - [MetaPhlAn3](#metaphlan3) - Genome-level marker gene based taxonomic classifier
- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling. - [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 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - [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` - `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. - `<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.
</details> </details>
The following report files are used for the taxpasta step: The following report files are used for the taxpasta step: