anvi'o analysis of SGG metagenomes

##Scripts used to process SGG metagenomes (Chapters 4 and 5 of my PhD thesis).

1. qc_trimmed_nonjob.sh uses fastp (https://github.com/OpenGene/fastp) to quality filter and merge Illumina paired-end reads.

2. merge_fastqs.sh simply concatenates fastq.gz files.

3. anvio_import_final.sh uses anvi'o (https://github.com/merenlab/anvio) to

   1. re-format assembled .fasta files,
   2. generate a contigs database,
   3. determine single-copy genes from trained HMMs,
   4. find COGs for and taxonomically classify contigs using kaiju (https://github.com/bioinformatics-centre/kaiju),
   5. mapping raw reads to contigs using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml),
   6. bin contigs using CONCOCT (https://github.com/BinPro/CONCOCT) and
   7. manually refine bins. Based on anvi'o tutorials available at http://merenlab.org/2016/06/22/anvio-tutorial-v2/.

4. anvio_pangenomics.sh uses anvi'o to create FeOB, SOB pangenomes and analyse them.

5. anvio_omnitrophica_pangenomics.sh uses ncbi-genome-download (https://github.com/kblin/ncbi-genome-download) and anvi'o to create Omnitrophica, Cand. Methanoperedens pangenomes and compare them to external GTDB genomes using ANIb.

Install megatools

Follow instructions on here.

Set up MEGA credentials

mega-login [EMAIL] [PASSWORD]

Check out MEGA cloud directories

mega-ls SGG_metagenomes/data/anvio_sgg_mag_processing

Download files from MEGA cloud

mega-get SGG_metagenomes/data/anvio_sgg_mag_processing/anvio_import_final.sh