Appendices

1 Using wget

1.1 Download the entire Workshop directory?!

https://cgr.liv.ac.uk/454/acdarby/LIFE750

have a look at the directly tree.

wget \
  --recursive \
  --no-parent \
  --no-host-directories \
  --cut-dirs=3 \
  https://cgr.liv.ac.uk/454/acdarby/LIFE750/Workshops/

What each flag does:

  • --recursive: follow links
  • --no-parent: do not climb above Workshops
  • --no-host-directories: do not create cgr.liv.ac.uk/...
  • --cut-dirs=3: strip 454/acdarby/LIFE750
  • Trailing / is important

1.2 Download only a specific subdirectory

wget \
  --recursive \
  --no-parent \
  --no-host-directories \
  --cut-dirs=4 \
  https://cgr.liv.ac.uk/454/acdarby/LIFE750/Workshops/7-Binning/

2 Appendix A: Resources and data

  • KrakenTools: https://github.com/jenniferlu717/KrakenTools
  • MAG assembly review: https://www.sciencedirect.com/science/article/pii/S2001037021004931
  • Genome-resolved metagenomics review: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab030/6184411
  • bioBakery tools: https://github.com/biobakery/biobakery
  • Functional annotation comparison: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6289-6
  • MicrobeAnnotator: https://github.com/cruizperez/MicrobeAnnotator
  • MetaEuk: https://github.com/soedinglab/metaeuk
  • Metagenomic visualisation methods: https://www.researchgate.net/publication/318252633_Methods_for_The_Metagenomic_Data_Visualization_and_Analysis
  • Visualisation review: https://www.sciencedirect.com/science/article/pii/S2001037024001430

Manuals:

  • Conda: https://conda.io/projects/conda/en/latest/user-guide/getting-started.html
  • FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • MultiQC: https://multiqc.info/
  • Trim Galore: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
  • Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
  • BBTools: https://jgi.doe.gov/data-and-tools/bbtools/
  • Kraken2: https://github.com/DerrickWood/kraken2/wiki/Manual
  • Krona: https://github.com/marbl/Krona/wiki/KronaTools
  • Bracken: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
  • LEfSe: https://huttenhower.sph.harvard.edu/lefse/
  • HUMAnN: https://huttenhower.sph.harvard.edu/humann/
  • MetaPhlAn: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4
  • MegaHit: https://github.com/voutcn/megahit
  • MetaBAT2: https://bitbucket.org/berkeleylab/metabat/src/master/
  • CheckM: https://github.com/Ecogenomics/CheckM/wiki
  • Prokka: https://github.com/tseemann/prokka
  • MinPath: https://github.com/mgtools/MinPath
  • MetaCyc: https://metacyc.org/

Obtaining read data

wget -O K1_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505102/ERR505102_1.fastq.gz
wget -O K1_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505102/ERR505102_2.fastq.gz
wget -O K2_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505104/ERR505104_1.fastq.gz
wget -O K2_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505104/ERR505104_2.fastq.gz
wget -O K3_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505095/ERR505095_1.fastq.gz
wget -O K3_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505095/ERR505095_2.fastq.gz
wget -O K4_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505096/ERR505096_1.fastq.gz
wget -O K4_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505096/ERR505096_2.fastq.gz
wget -O K5_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505097/ERR505097_1.fastq.gz
wget -O K5_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505097/ERR505097_2.fastq.gz
wget -O K6_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505098/ERR505098_1.fastq.gz
wget -O K6_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505098/ERR505098_2.fastq.gz
wget -O K7_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505099/ERR505099_1.fastq.gz
wget -O K7_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505099/ERR505099_2.fastq.gz
wget -O K8_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505100/ERR505100_1.fastq.gz
wget -O K8_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505100/ERR505100_2.fastq.gz
wget -O K9_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505101/ERR505101_1.fastq.gz
wget -O K9_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505101/ERR505101_2.fastq.gz
wget -O K10_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505103/ERR505103_1.fastq.gz
wget -O K10_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505103/ERR505103_2.fastq.gz
wget -O K11_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505105/ERR505105_1.fastq.gz
wget -O K11_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505105/ERR505105_2.fastq.gz
wget -O K12_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505106/ERR505106_1.fastq.gz
wget -O K12_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505106/ERR505106_2.fastq.gz
wget -O W1_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505090/ERR505090_1.fastq.gz
wget -O W1_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505090/ERR505090_2.fastq.gz
wget -O W2_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505088/ERR505088_1.fastq.gz
wget -O W2_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505088/ERR505088_2.fastq.gz
wget -O W3_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505084/ERR505084_1.fastq.gz
wget -O W3_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505084/ERR505084_2.fastq.gz
wget -O W4_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505085/ERR505085_1.fastq.gz
wget -O W4_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505085/ERR505085_2.fastq.gz
wget -O W5_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505086/ERR505086_1.fastq.gz
wget -O W5_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505086/ERR505086_2.fastq.gz
wget -O W6_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505087/ERR505087_1.fastq.gz
wget -O W6_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505087/ERR505087_2.fastq.gz
wget -O W7_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505089/ERR505089_1.fastq.gz
wget -O W7_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505089/ERR505089_2.fastq.gz
wget -O W8_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505091/ERR505091_1.fastq.gz
wget -O W8_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505091/ERR505091_2.fastq.gz
wget -O W9_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505092/ERR505092_1.fastq.gz
wget -O W9_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505092/ERR505092_2.fastq.gz
wget -O W10_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505093/ERR505093_1.fastq.gz
wget -O W10_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505093/ERR505093_2.fastq.gz
wget -O W11_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505094/ERR505094_1.fastq.gz
wget -O W11_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505094/ERR505094_2.fastq.gz
wget -O W12_R1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505083/ERR505083_1.fastq.gz
wget -O W12_R2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR505/ERR505083/ERR505083_2.fastq.gz