Example reference FASTAs

This page shows a couple of example reference FASTAs for Badread. They use depth= and circular= to control how Badread behaves. The ... lines aren't part of the FASTA, they just mean 'more sequence'.

Example bacterial genome reference FASTA

>chromosome depth=1.0 circular=true
GTGTCACTTTCGCTTTGGCAGCAGTGTCTTGCCCGATTGCAGGATGAGTTACCAGCCACAGAATTCAGCA
...
>plasmid depth=1.3 circular=true
ATGACGAGCGAAAATAACAGCTTACTTCTGAACCTTCAGGAAGTTGATAAGACAACCGGCGAAGTTGTTA
...

Example eukaryote genome reference FASTA

>chromosome_I depth=1.0
CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACA
...
>chromosome_II depth=1.0
AAATAGCCCTCATGTACGTCTCCTCCAAGCCCTGTTGTCTCTTACCCGGATGTTCAACCAAAAGCTACTT
...
>chromosome_III depth=1.0
CCCACACACCACACCCACACCACACCCACACACCACACACACCACACCCACACACCCACACCACACCACA
...
>mitochondria depth=100.0 circular=true
TTCATAATTAATTTTTTATATATATATTATATTATAATATTAATTTATATTATAAAAATAATATTTATTA
...

If you want to be explicit, you can include circular=false in the headers for linear sequences. But Badread assumes linearity by default, so you can just leave it out (as shown with the eukaryote example's chromosomes).