Add multiple regions analysis / 5R / SMURF / q2-sidle

.github/workflows/ci.yml

@@ -57,6 +57,7 @@ jobs:
           - "test_pacbio_its"
           - "test_sintax"
           - "test_pplace"
+          - "test_multiregion"
         profile:
           - "docker"
 

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#700](https://github.com/nf-core/ampliseq/pull/700) - Optional `--save_intermediates` to publish QIIME2 data objects (.qza) and visualisation objects (.qzv)
+- [#702](https://github.com/nf-core/ampliseq/pull/702) - Add multiple regions analysis (including 5R / SMURF / q2-sidle)
 
 ### `Changed`
 

CITATIONS.md

@@ -103,6 +103,24 @@
 
   > Czech, Lucas, Pierre Barbera, and Alexandros Stamatakis. “Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data.” Bioinformatics 36, no. 10 (May 1, 2020): 3263–65. https://doi.org/10.1093/bioinformatics/btaa070.
 
+### Multi region analysis (also include Greengenes 13_8 or SILVA 128)
+
+- [q2-sidle](https://doi.org/10.1101/2021.03.23.436606)
+
+  > Debelius, J.W.; Robeson, M.; Lhugerth, L.W.; Boulund, F.; Ye, W.; Engstrand, L. "A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution." Preprint in BioRxiv. doi: 10.1101/2021.03.23.436606
+
+- [SMURF](https://doi.org/10.1186/s40168-017-0396-x)
+
+  > Fuks, G.; Elgart, M.; Amir, A.; Zeisel, A.; Turnbaugh, P.J., Soen, Y.; and Shental, N. (2018). "Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling." Microbiome. 6: 17. doi: 10.1186/s40168-017-0396-x
+
+- [RESCRIPt](https://doi.org/10.1371/journal.pcbi.1009581)
+
+  > Robeson MS 2nd, O'Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol. 2021 Nov 8;17(11):e1009581. doi: 10.1371/journal.pcbi.1009581. PMID: 34748542; PMCID: PMC8601625.
+
+- [SEPP](https://doi.org/10.1128/msystems.00021-18)
+
+  > Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 2018 Apr 17;3(3):e00021-18. doi: 10.1128/mSystems.00021-18. PMID: 29719869; PMCID: PMC5904434.
+
 ### Downstream analysis
 
 - [QIIME2](https://pubmed.ncbi.nlm.nih.gov/31341288/)

README.md

@@ -21,7 +21,7 @@
 
 ## Introduction
 
-**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.
+**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Multiple region analysis such as 5R is implemented. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.
 
 A video about relevance, usage and output of the pipeline (version 2.1.0; 26th Oct. 2021) can also be found in [YouTube](https://youtu.be/a0VOEeAvETs) and [billibilli](https://www.bilibili.com/video/BV1B44y1e7MM), the slides are deposited at [figshare](https://doi.org/10.6084/m9.figshare.16871008.v1).
 

assets/schema_input.json

@@ -12,7 +12,7 @@
                 "pattern": "^[a-zA-Z][a-zA-Z0-9_]+$",
                 "unique": true,
                 "errorMessage": "Unique sample ID must be provided: Must start with a letter, and can only contain letters, numbers or underscores; Regex: '^[a-zA-Z][a-zA-Z0-9_]+$'",
-                "meta": ["id"]
+                "meta": ["sample"]
             },
             "forwardReads": {
                 "type": "string",

assets/schema_multiregion.json

@@ -0,0 +1,37 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/ampliseq/master/assets/schema_multiregion.json",
+    "title": "nf-core/ampliseq pipeline - params.multiregion schema",
+    "description": "Schema for the file provided with params.multiregion",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "region": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "unique": true,
+                "errorMessage": "Region name is mandatory, cannot contain spaces, and must be unique",
+                "meta": ["region"]
+            },
+            "region_length": {
+                "type": "integer",
+                "errorMessage": "Length of region must be an integer",
+                "meta": ["region_length"]
+            },
+            "FW_primer": {
+                "type": "string",
+                "pattern": "^[ATUGCYRSWKMBDHVN]*$",
+                "errorMessage": "FW_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
+                "meta": ["fw_primer"]
+            },
+            "RV_primer": {
+                "type": "string",
+                "pattern": "^[ATUGCYRSWKMBDHVN]*$",
+                "errorMessage": "RV_primer must be provided and may contain only uppercase nucleotide IUPAC code [ATUGCYRSWKMBDHVN]",
+                "meta": ["rv_primer"]
+            }
+        },
+        "required": ["region", "region_length", "FW_primer", "RV_primer"]
+    }
+}

bin/taxref_reformat_sidle.sh

@@ -0,0 +1,28 @@
+#!/bin/sh
+
+derep="$1"
+
+# Untar any tar file in the working directory
+tar xzf database.tar.gz
+
+# Greengenes 13_8
+if [ -d "gg_13_8_otus" ]; then
+    mv gg_13_8_otus/rep_set/${derep}_otus.fasta gg_13_8_otus_rep_set_${derep}_otus.seq.fasta
+    mv gg_13_8_otus/rep_set_aligned/${derep}_otus.fasta gg_13_8_otus_rep_set_aligned_${derep}_otus.alnseq.fasta
+    mv gg_13_8_otus/taxonomy/${derep}_otu_taxonomy.txt gg_13_8_otus_taxonomy_${derep}_otu_taxonomy.tax.txt
+    # remove uncompressed folder
+    rm -r gg_13_8_otus
+elif [ -d "SILVA_128_QIIME_release" ]; then
+    mv SILVA_128_QIIME_release/rep_set/rep_set_all/${derep}/${derep}_otus.fasta SILVA_128_QIIME_release_rep_set_all_${derep}_otus.seq.fasta
+    gunzip -c SILVA_128_QIIME_release/rep_set_aligned/${derep}/${derep}_otus_aligned.fasta.gz > SILVA_128_QIIME_release_rep_set_aligned_${derep}_otus_aligned.alnseq.fasta
+    mv SILVA_128_QIIME_release/taxonomy/taxonomy_all/${derep}/consensus_taxonomy_7_levels.txt SILVA_128_QIIME_release_taxonomy_all_${derep}_consensus_taxonomy_7_levels.tax.txt
+    # remove uncompressed folder
+    rm -r SILVA_128_QIIME_release
+else
+    echo "No expected directory detected"
+fi
+
+
+
+
+