TGatter

The problem arises on some machines as SPOA is compiled on a command set not compatible with the CPU. Likely this arises because of the "-march=native" in the SPOA make...

Yes, this is the case. File 1 ``` [thomas@vodka experimental]$ head -n 12 /scr/k70san2/thomas/yeast_nanopore/YeastStrainsStudy/fastqs/miseq/s288c_1.fastq @ERR1938683.1 MS5_18429:1:2113:11939:14368#1/1 GTGGTGTGTGGTGTGGTGTGTGGAGTGGTGGGGGGGTGGGGTGGGTGGGTGGGGAGTGGGGTGGTGAGGGGGTGTGGTGTGTGGGGGGGTGGGTGGGGAGGGGGGGGGGTGGGGGGGTGGGGGGGGGGGGTGGGGGGTGGGGGGGTGGGG + AAAAAAAA1CA1FFEEFFAEFGG101BF100A//AEEEEEE0AAAE0AAE0B0//-------99----9-----------;-9-------;-------9-9-9--9--/-----9----;-///9/- @ERR1938683.3 MS5_18429:1:2104:19853:5516#1/1 CACCACACCCACACACCCACACACCACACCCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCCCACACACACATCCTAACACTACCCTAACACAGCCCTAATCTAACCCTCCCCAACCTGTCTCTCAACTTA + BBB@BBBBBBBBGGGGFGGGGGEGGD222EEAECE2FGA1AEFGAE?FEGGCEAEGGGEEGDHAEEEE1GHHGGH11EE?/>EE/EEA///00/0?011111?1011000-.-000...

Thank you. I indeed did not think about this problem. As it seems, minimap2 and racon both remove the `/[0-9]` suffix, as they consider only the id to the first...

I now joined both Illumina files and assigned running ids for each read. The results now look better, but are overall still worse. This is consistent, independent of whether running...

I have tested the same setup using PILON, seeing only improvements. I tested even the same alignment files for both Racon and PILON, Racon worsening results but PILON improving them....

Hi. Yes. The organism/strain is exactly the same (Saccharomyces cerevisiae s288c). The fragmentation of the contigs is due to our method in development that is still missing a few components....