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Toy files originally collected for the MRC Climb workshop in the Gambia, January 2018
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_readme_maker
archives
files
misc
phage
scripts
README.md

README.md

Bioinformatics and the Linux Terminal

What it is

A list of example files to start using the Linux Command Line interface (CLI). Originally prepared for Bash for Bioinformatics training

History

  • 2019-02-20 Readme file generator added (_readme_maker/make_readme)
  • 2018-10-20 Added a "misc" subdirectory with examples taken from another training set
  • 2018-03-05 Package updated, "files" directory added
  • 2018-02-29 First release

Content

📁phage

A set of files to test parsing of bioinformatics format, mostly related to PhiX phage.

  • vir_assembly_stats.txt
  • vir_genomic.fna
  • GCF_000840245.1_ViralProj14204
  • md5checksums.txt
  • vir_feature_table.txt
  • vir_genomic.gff
  • annotation_hashes.txt
  • vir_cds_from_genomic.fna
  • vir_protein.gpff
  • README.txt
  • vir_translated_cds.faa
  • vir_genomic.gbff
  • vir_feature_count.txt
  • vir_rna_from_genomic.fna
  • vir_protein.faa
  • assembly_status.txt
  • vir_assembly_report.txt

📁archives

Archives to test decompression tools

  • archive.tar.gz
  • archive.zip

📁misc

This is an extra subdirectory, it contains its own README file for details

  • genbank
  • README.md
  • test
  • ecoli

📁files

Common file formats, both binary (e.g. PNG image) and text files (e.g. CSV). A PDF document is included to see how less can also handle them.

  • R-package-edgeR.pdf
  • wine.csv
  • edgeR.url
  • Sample.pdf
  • Green_Ok_Icon.png
  • cars.csv
  • introduction.txt

📁scripts

  • N50.pl
  • linkweb.sh
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