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!).