16SProcessingPipelinesWithQIIME2: Mock community analysis scripts

The scripts in this folder are associated with the following manuscript: Dacey, D.P., Chain, F.J.J. Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities. BMC Bioinformatics 22, 493 (2021). https://doi.org/10.1186/s12859-021-04410-2

1. Check raw quality scores, trim, merge, and concatenate sequences before Qiime 2 submission.

Calls on Check_sequence_quality.sh

source ./Check_sequence_quality_MultiJobSubmission.sh

2. Remove primers, trims, merges, merges/concats with cutadapt and pandaseq on paired end sequences.

Calls on TrimPrimersLengthQual_MergeConcat_PE.sh

source ./TrimPrimersLengthQual_MergeConcat_PE_MultiJobSubmission.sh

3. From the above primer removed and trimmed PE sequences perform full concatenation. No merging.

Calls on TrimPrimersLengthQual_ALLCONCAT.sh

source ./TrimPrimersLengthQual_ALLCONCAT_MultiJobSubmission.sh

4. FASTQ manifest creation - tells Qiime 2 what sequences to use.

Calls on fastq_manifest_filecreate_singleend.sh, fastq_manifest_filecreate_pairedend.sh, fastq_manifest_singleend.sh, and fastq_manifest_pairedend.sh.

source ./fastq_manifest_creator_MultiJobSubmission.sh

5. Metadata creation - links metadata to sequences.

Calls on Metadata_filecreate.sh and Metadata.sh scripts.

source ./Metadata_MultiJobSubmission.sh

Now that all input files are generated, submit to Qiime 2.

Classifiers for SILVA and Greengenes:

silva-132-99-nb-classifier.qza from https://data.qiime2.org/2020.2/common/silva-132-99-nb-classifier.qza

gg-13-8-99-nb-classifier.qza from https://data.qiime2.org/2020.2/common/gg-13-8-99-nb-classifier.qza

6. Runs submitted to DADA2 as single-end. May be considered single-end either because paired-end sequences were merged previously or they are true single-end (ie just R1 or just R2 sequences).

Calls on Qiime2_quality_dada2_tree_tax_biom_SE.sh.

source ./Qiime2_quality_dada2_tree_tax_biom_SE_MultiJobSubmission.sh

7. Runs submitted to DADA2 as paired-end, meaning these sequences were not merged beforehand and will have DADA2 perform merging. For some runs DADA2 may also perform trimming.

Calls on Qiime2_quality_dada2_tree_tax_biom_PE.sh and Qiime2_PL10_quality_dada2_tree_tax_biom_PE.sh.

source ./Qiime2_quality_dada2_tree_tax_biom_PE_MultiJobSubmission.sh

8. Modify and combine DADA2 stats tables from multiple pipelines. Need to manually modify header if don't want default dada2 stat headers.

Calls on Qiime2_export_tsv_dada2_stats.sh.

source ./Qiime2_export_tsv_dada2_stats_MultiJobSubmission.sh