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Add classifiers

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sofstam 2022-12-09 17:11:48 +01:00
parent c5f4c9486a
commit b35d26744d

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@ -20,6 +20,13 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [BBDuk](#bbduk) - Quality trimming and filtering for Illumina data
- [PRINSEQ++](#prinseq++) - Quality trimming and filtering for Illunina data
- [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
- [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) -
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
@ -105,6 +112,74 @@ fastp can automatically detect adapter sequences for Illumina data.
</details>
### Bowtie2
<details markdown="1">
<summary>Output files</summary>
- `bowtie2`
- `<sample_id>.bam`
- `<sample_id>.bowtie2.log`
- `<sample_id>.unmapped.fastq.gz`
</details>
### minimap2
<details markdown="1">
<summary>Output files</summary>
- `minimap2`
- `<sample_id>.bam`
</details>
### Samtools stats
<details markdown="1">
<summary>Output files</summary>
- `samtoolsstats`
- `<sample_id>.stats`
</details>
### cat
<details markdown="1">
<summary>Output files</summary>
- `cat`
</details>
### Kraken2
<details markdown="1">
<summary>Output files</summary>
- `kraken2`
- `<sample_id>.classified.fastq.gz`
- `<sample_id>.unclassified.fastq.gz`
- `<sample_id>.report.txt`
- `<sample_id>.classifiedreads.txt`
</details>
### KrakenUniq
<details markdown="1">
<summary>Output files</summary>
- `krakenuniq`
- `<sample_id>.classified.fastq.gz`
- `<sample_id>.krakenuniq.classified.txt`
- `<sample_id>.krakenuniq.report.txt`
- `<sample_id>.unclassified.fastq.gz`
## interleaved?
</details>
### MultiQC