readme: updated notes; added file for results archive

README.md

@@ -143,7 +143,8 @@ snakemake -s workflow_figures/Snakefile --cores 1 --configfile config/fig.yaml -
 
 Notes about manual analyses done using the generated data.
 
-- `gdb_mmseqs2_uniq_metat.md`: sample GDB, unique genes and their metaT coverage
 - `gdb_mmseqs2_highconf.md`: sample GDB, "high-confidence" proteins and protein clusters (assembly intersection and metaT cov.)
-- `gdb_rgi_aro3004454_flye.md`, `gdb_rgi_other.md`: sample GDB, RGI examples for diff. between SR/Hy and LR, and metaT coverage
-- `gdb_barrnap_metat.md`: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)
\ No newline at end of file
+- `gdb_rgi_aro3004454_flye.md`: sample GDB, an RGI example for diff. between SR/Hy and LR, and metaT coverage
+- ~~`gdb_mmseqs2_uniq_metat.md`: sample GDB, unique genes and their metaT coverage~~
+- ~~`gdb_rgi_other.md`: sample GDB, other RGI examples for diff. between SR/Hy and LR, and metaT coverage~~
+- ~~`gdb_barrnap_metat.md`: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)~~
\ No newline at end of file

README_ARCHIVE.md

+# About
+
+Results archive created for manuscript submission.
+
+# Archived files
+
+Abbreaviations and names:
+- sample names: Zymo, NWC, GDB, Rumen
+- SR: short-read (data)
+- LR: long-read (data)
+- Hy: hybrid (SR+LR)
+- metaG: metagenomic data
+- metaT: metatranscriptomic data
+  - only for GDB
+- metap: metaproteomic data
+  - only for GDB
+
+For each sample, the following files were saved (in `<sample>/results/`):
+- preprocessing stats:
+    - SR (metaG/metaT), FastP stats: `preprocc/*/sr/fastp.*`
+    - SR/LR (metaG/metaT, GDB), bbmap stats: `preproc/*/*/bbmap.*`
+- reads QC:
+  - SR (metaG/meetaT), FastQC: `qc/*/sr/*_fastqc.zip`
+  - LR, NanoStats: `qc/*/lr/NanoStats.*`
+- assembly
+  - "raw" contigs: `assembly/*/*/ASSEMBLY.fasta`
+  - polished contigs: `assembly/*/*/ASSEMBLY.POLISHED.fasta` (for LR and Hy only)
+    - polishing rounds: `assembly/*/*/POLISHING_*/ASSEMBLY.fasta`
+- assembly mapping
+  - BAM files: `mapping/*/*/*/ASSEMBLY.POLISHED.*.bam`
+  - mapping rate summary stats: `mapping/*/mappability.tsv`
+- annotation
+  - protein prediction w/ Prodigal
+    - FAA FASTA file: `annotation/prodigal/*/*/proteins.faa`
+    - summary (gene counts): `annotation/prodigal/summary.gene.counts.tsv`
+    - summary (summary gene length): `annotation/prodigal/summary.gene.length.tsv`
+  - AMR prediction w/ RGI (CARD)
+    - RGI output: `annotation/rgi/*/*/rgi.txt`
+    - summary: `annotation/rgi/summary.tsv`
+  - rRNA gene prediction w/ barrnap
+    - GFF file: `annotation/barrnap/*/*/*.gff`
+    - summary: `annotation/barrnap/summary.tsv`
+- analysis:
+  - assembly quality stats w/ QUAST
+    - QUAST report: `analysis/quast/*/*/report.tsv`
+    - sumamry: `analysis/quast/summary_report.tsv`
+  - analysis w/ Mash: `analysis/mash/contigs.*` (sketch and distances)
+  - DIAMOND search in UniProt database
+    - DIAMOND hits: `analysis/diamond/*.tsv`
+    - summary: `analysis/diamond/summary.db.tsv`
+  - protein clustering w/ mmseqs2
+    - clusters: `analysis/mmseqs2/clusters.tsv`
+    - summary: `analysis/mmseqs2/summary.tsv`
+- extra data/analysis for GDB:
+  - metaP reports: `metap/20210323/*_Default_Peptide_Report.txt`, `metap/20210323/*_Default_Protein_Report.txt`
+  - AMR/metaT analysis: `report/amr.tsv`
+  - "high-confidence" proteins: `report/mmseqs2_highconf.tsv`
+  - metaT cov. of exclusive proteins: `report/mmseqs2_uniq.tsv`
+  - metaP-based summary: `report/metap.txt`

README_REPROD.md

@@ -4,10 +4,6 @@ Notes for those trying to reproduce the results from the publication.
 
 # Setup
 
-Download
-- the code archive from XXX and extract it
-- GDB data from XXX
-
 Install `conda` and create the main `snakemake` environment (see `README.md`).
 
 Clone `OPERA-MS` repository