/paleocapture

Scripts associated with the article "Sediment Metagenomes as Time Capsules of Lake Microbiomes"

Primary LanguageHTMLMIT LicenseMIT

Sediment Metagenomes as Time Capsules of Lake Microbiomes

Pipelines and scripts associated with the article

Garner RE, Gregory-Eaves I, Walsh DA. 2020. Sediment Metagenomes as Time Capsules of Lake Microbiomes. mSphere 5:e00512-20. https://doi.org/10.1128/mSphere.00512-20.

Scripts

  1. 01_pipeline.md Bioinformatics pipeline that begins with raw metagenome reads, (1) trims the raw reads, (2) assembles metagenomes from the trimmed reads, and (3) maps trimmed reads to the metagenomes.
  2. 02_rnagenes.R Identify scaffolds containing conserved genes (ribosomal RNA or transfer rRNA genes) and count reads mapped (after removing scaffolds containing conserved genes).
  3. 03_idhist.R Read mapping vs. sequence identity in captured metagenomes.
  4. 04_genecontent.R Calculate gene counts on scaffolds in free and captured metagenomes.
  5. 05_covlength.R Scaffold coverage vs. length.
  6. 06_taxonomy.R Taxonomic analyses of free and captured metagenomes.
  7. 07_genera.R Gene counts for selected taxa in free metagenomes.
  8. 08_virusphylogeny.R Identify genes encoding Caudovirales terminase large subunit.
  9. 09_mapgenomes.R Map metagenome reads to reference reference genomes accessed from IMG.

Note on metagenome file names: Numeric codes sometimes stand in for lake names: Lac Paula 06-126, Eightmile Lake 17-054, Grand lac Touradi 17-067. Surface water metagenomes are named watercolumn, top sediment metagenomes top, and bottom sediment metagenomes bottom.