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Add documentation for output docs

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sofstam 2023-01-12 15:47:29 +01:00
parent 3b6be07623
commit 9f21181972
1 changed files with 22 additions and 17 deletions
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docs/output.md
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@ -64,6 +64,8 @@ fastp can automatically detect adapter sequences for Illumina data.
<summary>Output files</summary>
- `fastp`
- `<sample_id>.fastp.fastq.gz`: File with the trimmed unmerged fastq reads.
- `<sample_id>.merged.fastq.gz`: File with the reads that were successfully merged.
</details>
@ -95,7 +97,7 @@ Note that the FASTQ files may _not_ always be the 'final' reads that go into tax
<summary>Output files</summary>
- `porechop`
- `<sample_id>.fastq.gz`
- `<sample_id>.fastq.gz`: Adapter-trimmed file
</details>
@ -143,8 +145,8 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
<summary>Output files</summary>
- `filtlong`
- `<sample_id>_filtered.fastq.g`
- `<sample_id>_filtered.log`
- `<sample_id>_filtered.fastq.gz`: Quality or short read data filtered file
- `<sample_id>_filtered.log`: log file containing summary statistics
</details>
@ -174,7 +176,7 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
<summary>Output files</summary>
- `minimap2`
- `<sample_id>.bam`
- `<sample_id>.bam`: Alignment file in bam format
</details>
@ -184,7 +186,7 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t
<summary>Output files</summary>
- `samtoolsstats`
- `<sample_id>.stats`
- `<sample_id>.stats`: File containing samtools stats output
</details>
@ -256,10 +258,11 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
<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`
- `<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.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.unmapped.fastq.gz`: Fastq file containing all unmapped reads
</details>
@ -269,7 +272,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
<summary>Output files</summary>
- `kaiju`
- `<sample_id>.tsv`
- `<sample_id>.tsv`: A file that summarises the fraction abundance, taxonomic ID, number of reads and taxonomic names
- `kaiju_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `kaiju2table`)
</details>
@ -279,8 +283,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply `
<summary>Output files</summary>
- `diamond`
- `<sample_id>.log`
- `<sample_id>.sam`
- `<sample_id>.log`: A log file containing stdout information
- `<sample_id>.sam`: A file in SAM format that contains the aligned reads
</details>
@ -328,8 +332,9 @@ The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. T
<summary>Output files</summary>
- `motus`
- `<sample_id>.log`
- `<sample_id>.out`
- `<sample_id>.log`: A log file that contains summary statistics
- `<sample_id>.out`: A classification file that summarises taxonomic identifiers, by default at the rank of mOTUs (i.e., species level), and their relative abundances in the profiled sample.
- `motus_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `motus_merge`)
</details>
### Krona