Comments (3)
It would be better to use -l0
which is develped for haploid assembly.
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Thank you very much for your suggestion. We only used hifi data, and after adding the -l 0 parameter, the result showed that the genome was 10M in multiple places and contig increased. Based on this result, we added the - s 0.35, -D 10 and -N 150 parameters, which did not improve the result. Can you give me some advice? The species in this study was approximately 54M in size, haploid, and 50% repetitive sequence
from hifiasm.
from hifiasm.
Related Issues (20)
- Switch error on X and Y chromosome HOT 2
- *.ovlp.bin file HOT 1
- Resolving switching error (?)
- Interchromosomal misjoin HOT 1
- Read error correction does not reduce the number of kmers present once, twice or three times
- Recreate p_ctg from p_utg HOT 3
- In the diploid assembly, hfiiasm identified a value that did not exist in the k-mer plot as the "homozygous read coverage threshold".
- fungi diploid assemble phasing errors
- What is the strategy for Ultra-long ONT integration? HOT 3
- No further progress after generating *bin files HOT 1
- Issues with Hexaploid Assembly
- Numerous spurious contig overlaps in assemblies HOT 1
- output GFA with J lines in scaffolding mode
- Output that maps repeat shrapnels to unitigs and to scaffolded chromsomes
- High Duplication in my Assembly...l3 (purge-dup) doesn't help much HOT 1
- How to classify hifi reads into haplotype genomes? minimap2 did not work well HOT 2
- False inserts over duplicated regions (TRBV12-3/4) HOT 2
- Whether unitig will be filtered based on the hic signal of unitig HOT 2
- Hifiasm Assembly Purging
- "c" suffix on contigs
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