Failed Assembly / Extremely small contig

[cebos]

Hi ndierckx,
I have been trying to use NOVOPlasty to assemble a mitochondrial genome from illumina PE short read data, and despite many runs tweaking all parameters I have only managed to have the program output 1 contig each time, ranging in size from 140-158bp (The published assembly for an individual from the same species is 17519 bp).
I've attached the extended log file and the slurm script for my latest NOVOPlasty run.
Thanks for your help!

log_extended_Anilany_helenae_FGZC899_3.15.23.txt
slurm-300249.out.txt

[ndierckx]

Hi,

Sorry I forgot to answer, you need to use a proper seed sequence, not just the reference sequence, because it will start the assembly from the beginning of that fasta file, which is probably not conserved or is repetitive. Just cut 500 bp or so from the middle of that reference file and use that as a seed, or use a COI gene sequence from a related species...