Table 2.

Description of the Primary Hybracter Output Files

Output File	Description
{sample}_final.fasta	Final assembly FASTA file for the sample. Contains all chromosome(s) and plasmids for complete isolates and all contigs for incomplete isolates.
{sample}_chromosome.fasta	Final assembly FASTA file for the chromosomes(s) in a complete sample.
{sample}_plasmid.fasta	Final assembly FASTA file for the plasmids in a complete sample.
hybracter_summary.tsv	A TSV file combining the {sample}_summary.tsv files for all samples.
{sample}_summary.tsv	A TSV file containing columns denoting for the sample:  • Assembly completeness  • Total assembly length  • Number of contigs assembled  • The polishing round deemed to be most accurate and selected as the final assembly  • The length of the longest contig  • The estimated coverage of the longest contig  • The number of circular plasmids recovered by Plassembler
{sample}_per_contig_stats.tsv	A TSV file containing columns denoting for the sample:  • Contig name  • Contig Type (chromosome or plasmid) (complete samples only)  • Contig length  • Contig GC%  • Contig circularity (complete samples only)