Nguyen Thanh Nguyen

> Hi, > > The reads are used to identify misassemblies in the assembly before scaffolding. First, assembly is aligned to the reference and all alignment breakpoints are identified. Then...

Hi, I'm still waiting for my question about scaffolder. @chiu-shenpo I think your topic is a totally different with what I'm asking, you should have opened another issue to avoid...

Of course, it does matter, and I thank you for pointing that out. However, let be clear here, if you open another issue, then more people will acknowledge the situation,...

Thanks! I will try it out. However, I still don't understand why the long read subsampling produces the same file despite using 2 different long read files, or different subsampling...

After changing k=19 according to kmergenie, I got another error: `ERROR: "haslr_assemble" returned non-zero exit status`

[NA12878_R1_15X_merge_kmer.dat.pdf](https://github.com/vpc-ccg/haslr/files/5449620/NA12878_R1_15X_merge_kmer.dat.pdf) @jelber2 hi, this is the histogram of kmer size @haghshenas thank you for your support. I suspect that the problem come from using `cat` on fastq.gz file of CCS....

hi @haghshenas, I re-downloaded the Long read file, this time I use sra-toolkit to download the SRA files, then convert them to fastq to make sure all files are well-preserved....

for checking integrity of Long read fastq file, I aligned it to HG38 using minimap2, the coverage is around 30X, as expected. 

I also encountered this problem in using conda version, everything run fine but there's no final output ``` haslr.py -t 6 -g 3g -l /mnt/Data/GIAB/NA12878/FASTQ_Illumina/HG001.m64011_190326_191011.consensusreads.fastq.gz -x pacbio -s /mnt/Data/GIAB/NA12878/FASTQ_Illumina/U0a_CGATGT_L001_R1_001.fastq.gz /mnt/Data/GIAB/NA12878/FASTQ_Illumina/U0a_CGATGT_L001_R2_001.fastq.gz...

Hi @tanghaibao , the xHLA run great, however I also want to check if the updated database from IMGT can lead to different typing result. Could you please help showing...