zhangrengang

How to generate multi-samples kmer count table?

10

Hi, I want a count table (m× n) like this: |# kmer seq | sample1 |sample2 | ...| |---|---|---|---| |AAA...|1|2|...| |AAC...|0|5|...| |AAG...|4|2|...| where m is number of samples or individuals...

Not support very long chromosomes?

8

## Expected Behavior `metaeuk` run normally with other genomes, but crash with a large pine genome (Pinus tabuliformis, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA784915). Do it not support the very long chromosomes: ``` $ head...

``` Traceback (most recent call last): File "Stats.py", line 16, in fisher_test try: pval = fisher.pvalue(x11, x12, x21, x22).right_tail File "src/cfisher.pyx", line 86, in cfisher.pvalue OverflowError: value too large to...

I have get as long as ~500K bp gaps when using PacBio reads for scaffolding. However, the long reads are not longer than 80K. I wonder how such long gaps...

When I count kmers for a large BAM file (586 Gb), KMC froze with CPU% = 0. The following is the log: ``` + kmc -fbam -k19 -t32 -m256 -ci1...

Hi, I checked the unitig graph and found many short tips with very low coverage depth (< 10x). Perhaps due to this reason, the haplotype contigs were fragmented (N50 <...