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Update output.md

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sofstam 2022-12-12 17:06:05 +01:00
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@ -23,10 +23,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [Bowtie2](#bowtie2) - Host removal for Illumina reads
- [minimap2](#minimap2) - Host removal for Nanopore reads
- [samtoolsstats](#samtoolsstats) - Statistics from host removal
- [cat] - **WIP**
- [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
- [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
- [Bracken](#bracken) -
- [Centrifuge](#centrifuge) - Taxonomic classifier that uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
- [Kaiju](#kaiju) - Taxonomic classifier that finds maximum (in-)exact matches on the protein-level.
- [Diamond](#diamond) - Sequence aligner for protein and translated DNA searches.
- [mOTUs](#motus) - Tool for marker gene-based OTU (mOTU) profiling.
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@ -145,15 +148,6 @@ fastp can automatically detect adapter sequences for Illumina data.
</details>
### cat
<details markdown="1">
<summary>Output files</summary>
- `cat`
</details>
### Kraken2
<details markdown="1">
@ -182,9 +176,51 @@ fastp can automatically detect adapter sequences for Illumina data.
</details>
### Centrifuge
<details markdown="1">
<summary>Output files</summary>
- `centrifuge`
- `<sample_id>.centrifuge.mapped.fastq.gz`
- `<sample_id>.centrifuge.report.txt`
- `<sample_id>.centrifuge.results.txt`
- `<sample_id>.centrifuge.unmapped.fastq.gz`
</details>
### Kaiju
<details markdown="1">
<summary>Output files</summary>
- `kaiju`
- `<sample_id>.tsv`
</details>
### Diamond
<details markdown="1">
<summary>Output files</summary>
- `diamond`
- `<sample_id>.log`
- `<sample_id>.sam`
</details>
### mOTUs
<details markdown="1">
<summary>Output files</summary>
- `motus`
- `<sample_id>.log`
- `<sample_id>.out`
</details>
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>>>>>>> 6d0b5d0a58d92fabfc239818f272bb06cfeb1e66
### MultiQC
<details markdown="1">