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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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the question about nd.asm.p.fasta #96

Closed WenhaoLiu0218 closed 3 years ago

WenhaoLiu0218 commented 3 years ago

Dear author，

i finished the final assembly using NextDenovo (v2.3.0). I found the file nd.asm.p.fasta in 01.ctg_graph.sh.work/ctg_graph0, my question is what's the difference between this file and the final assembly result nd.asm.fasta. By using the old version, i can get some assembly results and choose the best one through them, but i could not find these files in the new version, and the N50 length of nd.asm.p.fasta is longer than N50 of nd.asm.fasta, although the BUSCO result is a little bit low, i wonder whether i can chose nd.asm.p.fasta as the final assembly result or not? Thanks!

moold commented 3 years ago
  1. In theroy, nd.asm.p.fasta contains more structural & base errors than nd.asm.fasta, you also can chose nd.asm.p.fasta as the final assembly result, but be careful about the assembly quality.
  2. Too many users complained that they didn't know how to choose the assembly result, so I removed this function, you can change the assembly parameters in nextgraph_options manually, and rerun it. NextDenovo will skip the previous steps and only run the last step.
WenhaoLiu0218 commented 3 years ago

Thanks for replying! I will try to change assembly parameters.

Barbossa-V commented 3 years ago

Dear author， I try to assemble some scafolds from metagemomic. The file 'input.fofn' contain three fasta-format file. But I 've failed in the 'assemble 'step when using ’nextgraph‘. I 've found that the nd.asm.p.fastq file is [null]! But the input file for nextgraph is normal, including '01.ctg_graph.input.seqs' and '01.ctg_graph.input.ovls' . How can I adjust parameters of 'nextgraph', can you give me some suggest ，please ？ Thank you very much.

moold commented 3 years ago

NextDenovo is not suitabale for metagemomic, because it assumes the genome has a uniform depth of coverage. But if you still want to have a try, you can set seed_depth=1000. Besides, I will close this issue, if you still have problem, you need to open a new issue because your question is not related to this issue.

Barbossa-V commented 3 years ago

Thank you very much! my parameters are： read_cutoff = 0.2k ，genome_size = 100g，seed_depth = 1，seed_cutoff = 3k，blocksize = 1g，minimap2_options_raw = -x ava-pb --minlen 20 --minmatch 20 -x ava-pb -t 4，nextgraph_options = -a 1 -E 200