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Add host removal outputs to table and bold all main directories in th…
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@gregorysprenger
gregorysprenger authored Jan 26, 2024
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Showing 1 changed file with 10 additions and 6 deletions.
16 changes: 10 additions & 6 deletions docs/output.md
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Expand Up @@ -44,23 +44,27 @@ _Note: \<Assembler\> is the name of the assembler (SPAdes, SKESA) given to `--as
| | \<SampleName\>-\<Assembler\>.SNPs-corrected.cnt.txt | Each line represents number of corrected SNPs (per correction round) |
| | \<Num\>of3-asm-attempt-failed.spades.log | Output log of SPAdes for each attempt tried (up to 3) |
| <a id="qa">Assembly/QA</a> | | **Quality Assurance files** |
| Assembly/QA/\<SampleName\> | | Output directory for each \<SampleName\> |
| Assembly/QA/\<SampleName\> | | **Output directory for each \<SampleName\>** |
| | \<SampleName\>-\<Assembler\>.CleanedReads-Bases.tsv | Number of cleaned bases |
| | \<SampleName\>-\<Assembler\>.GenomeCoverage.tsv | Genome Coverage |
| | \<SampleName\>-\<Assembler\>.QuastSummary.tsv | Quast Summary |
| <a id="ssu">SSU</a> | | **Small Subunit (16S) files** |
| | 16S-top-species.tsv | Top BlAST hit results |
| | 16S.\<SampleName\>-\<Assembler\>.fa | Top BLAST hit in FastA format |
| SSU/BLAST | | BLAST output files |
| SSU/BLAST | | **BLAST output files** |
| | \<SampleName\>-\<Assembler\>.blast.tsv.gz | BLAST output |
| <a id="trim-reads">CleanedReads</a> | | **Trimmed Reads** |
| | \<SampleName\>\_{R1,R2}.paired.fq.gz | Cleaned paired reads |
| | \<SampleName\>.single.fq.gz | Cleaned single read |
| CleanedReads/FLASH | | FLASH Output |
| CleanedReads/FLASH | | **FLASH Output** |
| | \<SampleName\>.clean-reads.tsv | Number of cleaned reads |
| | \<SampleName\>.overlap.tsv | Number of overlapping reads |
| CleanedReads/Trimmomatic | | Trimmomatic Output |
| CleanedReads/Trimmomatic | | **Trimmomatic Output** |
| | \<SampleName\>.trimmomatic.tsv | Discarded reads and singletons |
| CleanedReads/Hostile | | **Hostile host removal output** |
| | \<SampleName\>.Summary.Hostile-Removal.tsv | Summary of discarded reads and number of reads for downstream processes |
| CleanedReads/SRA-Human-Scrubber | | **SRA Human Scrubber host removal output** |
| | \<SampleName\>.Summary.SRA-Human-Scrubber-Removal.tsv | Summary of discarded reads and number of reads for downstream processes |
| <a id="summaries">Summaries</a> | | **Output Summaries** |
| | Summary.16S.tab | Top BLAST hit results |
| | Summary.Assemblies.tab | Contig summary information |
Expand All @@ -73,10 +77,10 @@ _Note: \<Assembler\> is the name of the assembler (SPAdes, SKESA) given to `--as
| | Summary.PhiX.tsv | Information on the removal of PhiX reads |
| | Summary.QC_File_Checks.tab | QC file checks |
| <a id="taxonomy">Taxonomy</a> | | **Taxonomic Classification** |
| Taxonomy/kraken/\<SampleName\> | | Kraken Output for each \<SampleName\> |
| Taxonomy/kraken/\<SampleName\> | | **Kraken Output for each \<SampleName\>** |
| | \<SampleName\>.kraken_output.tab.gz | Full Kraken output |
| | \<SampleName\>.kraken_summary.tsv | Summarized unclassified, top 2 genus and top 2 species information |
| Taxonomy/kraken2/\<SampleName\> | | Kraken2 Output for each \<SampleName\> |
| Taxonomy/kraken2/\<SampleName\> | | **Kraken2 Output for each \<SampleName\>** |
| | \<SampleName\>.kraken_output.tab.gz | Full Kraken2 output |
| | \<SampleName\>.kraken2_summary.tsv | Summarized unclassified, top 2 genus and top 2 species information |
| <a id="log">pipeline_info</a> | | **Log files** |
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