This version is the first draft version of the code for publication. This version of the code resulted from re-running the entire ArcDyn pipeline from the beginning (i.e. from the original sequence files received from sequencing centre). The scripts here represent Step 4 in Box 1 of the SPIKEPIPE paper.
-
downloading and concatenating the fastq files for each sample
-
TrimGalore to remove adapters and filter out bad reads
-
fastQC and multiQC to generate summary statistics
-
minimap2 and samtools to map reads to mitogenomes and barcodes and to filter the bam files, also run bedtools to calculate coverage per position
-
merge and process the idxstats and genomecov files, merge by Run, and generate input data files for statistical analysis.
-
The statistical analysis code and the input data files for statistical analysis are in 7_ecological_analysis/.
-
reference files for use above (reference mitogenomes and barcodes, sample metadata, and taxonomy information for the mitogenomes and barcodes)
Created on 20180126