Hu Jiang
Hu Jiang
Pls provide more details as https://github.com/Nextomics/NextDenovo/issues/new?assignees=&labels=&template=bug-or-error-report.md&title=
Could you check whether all files in /data/01/user152/nextdenovo/new_01_rundir/03.ctg_graph/01.ctg_graph.input.seqs are not empty? and also use `samtools faidx` to check idx files are correct. BTW, pls provide your system and gcc version.
Just check the first few lines and you will see that idx files are similar with the result of samtools faidx.
1. I do not recommend using these two types of data together for assembly, although you can do so, and NextDenovo will treat all data as ONT or CLR data...
Hi, 1, No, although NextDenovo will try to correct reads with length longer than 1001bp, but it will filter some low quality, low depth reads and..., so the output corrected...
Yes, but I recommend using bin/seq_stat to calculate the expected seed cutoff.
Hi, the input data is not enough, and the seed length is too short, you can see the default value of option -min_len_seed in nextcorrect.py is 10k, so most of...
NextDenovo is only an assembly software, so if you need a more accuracy assembly, you can try to [NextPolish](https://github.com/Nextomics/NextPolish)
1. NO, the main purpose of this step is to correct structural errors, using mapping depth information and overlapped coordinates between seeds. 2. Yes.
I think, first, you need to map short genome reads or transcript reads to the assembly to check how many reads can be mapped in the assembly? May be the...