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ArcDyn files for the SPIKEPIPE pipeline
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0_s3cmdget
1_fastq_combine_script
2_trimgalore
3_fastQC
4_minimap2_samtools
5_idxstats_tabulate
6_referenceseqs_metadata
7_ecological_analysis
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README.md

README.md

ArcDyn

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

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