rspfau

NOVOPlasty3.8.3.pl

Yes, same result: [email protected]@TSU98054-LX:~/Desktop/second attempt geomys mitogenomes/TK24928/merged 2nd attempt$ perl ../../NOVOPlasty4.0.pl -c config.txt ----------------------------------------------- NOVOPlasty: The Organelle Assembler Version 4.0 Author: Nicolas Dierckxsens, (c) 2015-2020 ----------------------------------------------- Input parameters from the...

Here are the complete merged read files https://drive.google.com/file/d/1awqUKHKj_z24W5To_jUE38MmhhuQFNLs/view?usp=sharing

Yes, here it is [Geomys-pinetis-cytb-seed.txt](https://github.com/ndierckx/NOVOPlasty/files/4759055/Geomys-pinetis-cytb-seed.txt)

I tried a different seed, which I obtained by doing a local blast of the Illumina reads, and it worked without the memory issue--but still not enough depth to assemble...

And I've merged several other reads and haven't had any problems. It was somehow the combination of that particular merged read file and that particular seed file.

All files are attached. Thanks! [TK151508.zip](https://github.com/ndierckx/NOVOPlasty/files/4430653/TK151508.zip)

That is all the data we have--for now. The libraries were generated from multiple displacement amplification products, because we are having great difficulties due to NUMT contamination. https://www.qiagen.com/us/products/discovery-and-translational-research/pcr-qpcr/preamplification/repli-g/repli-g-mitochondrial-dna-kit/#orderinginformation There were...

Thanks! Heteroplasmy wasn't our main objective of the project--we just wanted complete mitogenome sequences free of NUMTs. NOVOplasty helped us accomplish that objective quite well--except for this last Illumina run,...

With this last Illumina run, we only successfully assembled mitogenomes from about half of our samples. I don't yet understand why, though, as some of the datasets are large. If...