Rob Murphy

@moold Hi, Do you mean do not do any form of cleaning on the raw reads, such as with bbtools before using in next polish here?

Thank you for the suggestions. I have a couple of questions: Is there any specific alignment tool you recommend I use? I was planning to use bowtie2. Secondly, I am...

Hi Dom, I mean that why does Blobtools operate via detecting comtamination in an already assembled genome vs before assembly? Would the down side of using an assembled genome not...

> before assembly there are only reads ... are you asking why are we not doing something with the reads? Yes. Would it be possible to use mapped raw reads...

Can confirm, this bug still exists in 2.1.3. Any insight in how to avoid it?

@KatharinaHoff This is just the standard `braker.gtf` output. I will check the exact version I am using. The exact command is: `braker.pl --cores=8 --fungus --genome=$input --prot_seq=$protDB --softmasking --workingdir=$outdir --species=$species --useexisting...

Here is the whole output for `braker.gtf` [PseudaA_sorted_masked.zip](https://github.com/Gaius-Augustus/BRAKER/files/6338457/PseudaA_sorted_masked.zip) Here is a combined out for : `cat GeneMark-EP/genemark.gtf augustus.hints.gtf > myNew.gtf` which Tomas suggested would be better for fungus [PseudaA_sorted_masked_combined.gtf.zip](https://github.com/Gaius-Augustus/BRAKER/files/6338465/PseudaA_sorted_masked_combined.gtf.zip)

@Juke34 Excellent :) So the conversions you have suggested of removing `longest isoforms` and` gtf > gff3` then `gff3 > embl` are all good to keep doing?

The error still occurs on the latest version of SPAdes

This is a slightly different version to the above. The forward and reverse reads are 27G each. I have allocated 178G with 16 cores. **SPAdes.log** [spades.log](https://github.com/ablab/spades/files/9239994/spades.log) **SPAdes version** 3.15.3 (not...