rebeccagarner/lakepulse16s

LakePulse16S

Scripts associated with the bioinformatic analysis of

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LakePulse 2017-2019 surface water 16S rRNA gene amplicon data (version lp2017-2019watercolumn16sreseq2_636lakes)

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Scripts

• 01-sample_list.R Generate sample list(s).
• 02-concatenate_fastq.sh Concatenate read files from the same samples.
• 03-cutadapt_2017/2018/2019.sh Trim primer sequences from raw demultiplexed reads.
• 04-plot_read_quality_dada2_2017/2018/2019.R Plot trimmed read quality.
• 05-filter_reads_dada2.R Filter and trim reads from the 3' end.
• 06-dada2_2017/2018/2019.R Infer amplicon sequence variants (ASVs) in dereplicated reads and merge forward and reverse paired-end reads.
• 07-combine_seqtabs_dada2.R Combine ASV tables and remove bimeric ASVs.
• 08-count_reads_fastq.sh Count number of reads in individual fastq files.
• 09-examine_nreads.R Track read loss through the pipeline.
• 10a-taxass_wf.txt Assign taxonomy (TaxAss workflow).
• 10b-reformat_dada2_seqtabs_modified.R Format ASV table for TaxAss.
• 11-format_asvs.R Format ASV and taxonomy tables.
• 12-align_asvs_mafft.txt Construct a de novo multiple sequence alignment.
• 12-align_asvs_sina.txt Align ASVs to SSU rRNA gene reference.
• 13-filter_asvs.R Filter ASVs.
• 14-curate_samples.R Filter ASVs based on taxonomy and filter samples.