miniasm
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lh3
Ultrafast de novo assembly for long noisy reads (though having no consensus step)
Hi there, Running miniasm with seemingly good contigs and mappings (below), I'm getting unitigs where all bases are N's. How can this be improved? Thanks! Example output ```.gfa```: ``` $...
Dear Dr. Li @lh3 What are, in your opinion, the main disadvantages of the algorithm of Miniasm compared to algorithms of more modern assemblers like Flye or Hifiasm? Best wishes,...
I am following these commands. However, I am getting blank output file. minimap2/minimap2 -x ava-pb -t8 pb-reads.fq pb-reads.fq | gzip -1 > reads.paf.gz # Layout miniasm/miniasm -f reads.fq reads.paf.gz >...
Hi, I used minimap2 get a paf file, and then I used miniasm to get the gfa file. It gave me the following error info. Could you give me any...
Hello, I have run the following commands: minimap2 -x ava-ont -t32 reads.fastq reads.fastq -K5M | gzip -1 > n_reads.paf.gz [M::mm_idx_gen::0.754*0.99] collected minimizers [M::mm_idx_gen::0.858*2.63] sorted minimizers [M::main::0.858*2.63] loaded/built the index for...
Hi lh3, I have minimap output, but no minisam output. The error may be because the first step of minisam: read 0 hits; stored 0 hits and 0 sequences. Can...
Hello, I'm trying to process my PacBio data, but I keep having problems with miniasm. I'm working on a computer with 24 cores and 120GB of RAM. I first used...
Hi, I observe that while I can manually draw out a single path between, say 5 reads, miniasm only generates a contig that has >2x read coverage at all locations...
in reference to https://github.com/lh3/miniasm/pull/81#issuecomment-608424107
main example had a typo (`pb-reads.fq` should be `reads.fq`)... was it intentional to see if user pays attention? :)