Bacterial training dataset for Galaxy training network tutorials on Genome assembly

This training dataset is from an imaginary Staphylococcus aureus bacterium with a miniature genome. There is a reference genome in various formats as well as some fastq reads of a closely related but also imaginary mutant strain.

It is a useful dataset for demonstrating:

• de novo genome assembly
• read mapping and variant calling
• genome annotation

The files included are:

• wildtype.fna: the reference genome sequence of the wildtype strain in fasta format (a header line, then the nucleotide sequence of the genome.)
• wildtype.gff: the reference genome sequence of the wildtype strain in general feature format (a list of features - one feature per line, then the nucleotide sequence of the genome.)
• wildtype.gbk: the reference genome sequence in genbank format.
• mutant_R1.fastq and mutant_R2.fastq: Fastq sequence reads of a closely related mutant strain.
  • The reads are paired-end.
  • Each read is 150 bases long.
  • The number of bases sequenced is equivalent to 19x the genome sequence of the wildtype strain. (Read coverage 19x - rather low!).