Table S1. Settings for running assembly in this study. 
SPAdes:
spades.py -1 <R1.fastq> -2 <R2.fastq> -o <path> -t 8 –careful
SKESA:
skesa –fastq <R1.fastq R2.fsatq> --cores 8 –contigs_out <path/file>
CLC:
Mapping options
Map reads back to contigs
Mapping mode:Map reads back to contigs (slow)
Update contigs:True Mismatch cost:2
Insertion cost:3
Deletion cost:3
Colorspace error cost:3
Length fraction:0.5
Similarity fraction:0.8
Colorspace alignment:True
Alignment mode:local
Match mode:random
Create list of un-mapped reads:True De novo options
Graph parameters
Automatic bubble size:True
Bubble size:50
Automatic word size:True
Word size:20 Contigs length
Minimum contigs length:200 Paired reads
Perform scaffolding:True Auto-detect paired distances:True