ABySS assembly: got unitig instead of contig

Question

[Phiphi]

Hello!

I have run ABySS (abyss-pe) command to assemble a de novo genome. I got only unitigs.fa file and not a contig.fa file. Is it normal? Thank you

commad: abyss-pe k=30 name=AA lib='MI.M03992_0274.001.BioOHT_59.AA_R2_Q20HL50 MI.M03992_0274.001.BioOHT_11.AA_R1_Q20HL50' \ MI.M03992_0274.001.BioOHT_11.AA_R1_Q20HL50='MI.M03992_0274.001.BioOHT_11.AA_R1_Q20HL50_R1.fq MI.M03992_0274.001.BioOHT_11.AA_R1_Q20HL50_R2.fq' MI.M03992_0274.001.BioOHT_59.AA_R2_Q20HL50='MI.M03992_0274.001.BioOHT_59.AA_R2_Q20HL50_R1.fq MI.M03992_0274.001.BioOHT_59.AA_R2_Q20HL50_R2.fq' \ se='MI.M03992_0274.001.BioOHT_11.AA_R1_Q20HL50_single.fq MI.M03992_0274.001.BioOHT_59.AA_R2_Q20HL50_single.fq'

Answer 1

[Carambakaracho]

Maybe abyss doesn't understand the library name. I'd try again with something like lib='BioOHT_59 BioOHT_11'. Other than that, your command looks fine, however I recommend using the Code (101/010 - button) formatting. The only thing is the k=30 option - is this the ideal kmer size? What read lengths do you use? What is the insert size of your PE library? Maybe unitigs is all abyss can do with your data.

[Phiphi]

@Carambakaracho

Thanks for your reply! I found it... That happens when something goes wrong during the assembly. Indeed, i got a error warning during the assembly.
I re-run my command fixing the mistake and it worked perfectly! Thank you!

[Carambakaracho]

I realized this had better been an answer. When a post is helpful a thumbs up is generally appreciated and will help others in the future to reevaluate an answer. In case the answer solved your problem, please mark it as accepted for pretty much the same reasons.