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docs/output.md
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@ -195,7 +195,7 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) or o
<summary>Output files</summary> <summary>Output files</summary>
- `minimap2` - `minimap2`
- `<sample_id>.bam`: Alignment file in bam format - `<sample_id>.bam`: Alignment file in BAM format
</details> </details>
@ -204,7 +204,7 @@ Note: minimap2 is not yet supported as a module in MultiQC and therefore there i
### Samtools stats ### Samtools stats
[Samtools stats](http://www.htslib.org/doc/samtools-stats.html) collects statistics from a SAM, `.bam`, or CRAM alignment file and outputs in a text format. [Samtools stats](http://www.htslib.org/doc/samtools-stats.html) collects statistics from a `.sam`, `.bam`, or `.cram` alignment file and outputs in a text format.
<details markdown="1"> <details markdown="1">
<summary>Output files</summary> <summary>Output files</summary>
@ -285,11 +285,11 @@ You will only receive the `.fastq` and `*classifiedreads.txt` file if you supply
<summary>Output files</summary> <summary>Output files</summary>
- `centrifuge` - `centrifuge`
- `<sample_id>.centrifuge.mapped.fastq.gz`: Fastq files containing all mapped reads - `<sample_id>.centrifuge.mapped.fastq.gz`: `FASTQ` files containing all mapped reads
- `<sample_id>.centrifuge.report.txt`: A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads - `<sample_id>.centrifuge.report.txt`: A classification report that summarises the taxonomic ID, the taxonomic rank, length of genome sequence, number of classified and uniquely classified reads
- `<sample_id>.centrifuge.results.txt`: A file that summarises the classification assignment for a read, i.e read ID, sequence ID, score for the classification, score for the next best classification, number of classifications for this read - `<sample_id>.centrifuge.results.txt`: A file that summarises the classification assignment for a read, i.e read ID, sequence ID, score for the classification, score for the next best classification, number of classifications for this read
- `<sample_id>.centrifuge.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample - `<sample_id>.centrifuge.txt`: A Kraken2-style report that summarises the fraction abundance, taxonomic ID, number of k-mers, taxonomic path of all the hits in the centrifuge run for a given sample
- `<sample_id>.centrifuge.unmapped.fastq.gz`: Fastq file containing all unmapped reads - `<sample_id>.centrifuge.unmapped.fastq.gz`: FASTQ file containing all unmapped reads
</details> </details>
@ -341,7 +341,7 @@ By default you will receive a TSV output. Alternatively, you will receive a `*.s
</details> </details>
The main output of MALT is the `.rma6` file format, which can be only loaded into MEGAN and it's related tools. We provide the `rma2info` text files for improved compatibility with spreadsheet programs and other programmtic data manipulation tools, however this has only limited information compared to the 'binary' RMA6 file format (the `txt` file only contains taxonomic ID and count, whereas RMA6 has taxonomic lineage information). The main output of MALT is the `.rma6` file format, which can be only loaded into MEGAN and it's related tools. We provide the `rma2info` text files for improved compatibility with spreadsheet programs and other programmtic data manipulation tools, however this has only limited information compared to the 'binary' RMA6 file format (the `.txt` file only contains taxonomic ID and count, whereas RMA6 has taxonomic lineage information).
You will only receive the `.sam` and `.megan` files if you supply `--malt_save_reads` and/or `--malt_generate_megansummary` parameters to the pipeline. You will only receive the `.sam` and `.megan` files if you supply `--malt_save_reads` and/or `--malt_generate_megansummary` parameters to the pipeline.