LJA
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AntonBankevich
Hello, thank you for developoing such a nice tool. I've run LJA on diploid lizard genome with this command `lja -t 150 --output-dir ./ --diploid --reads ./raw_reads/hifi/duni.ccs.common.fastq` and got error...
Using latest version of LJA (git cloned, cd into LJA, compiled with cmake version 3.18.2, gcc 8.2.0) on a Linux-based cluster, it looks like it runs all the way until...
Hi @AntonBankevich Thanks for the nice tool. I had some issues getting LJA to build using either Ubuntu21 (gcc 11.2) or CentOS (gcc 4.8). However I managed to find some...
Hello, Firstly, thank you for the development of a HiFi specific assembly tool! I was wondering if there are plans to modify the kmer selection parameter? Currently, the user has...
I have a similar case as of #17, #28. The assembly ran for ~11 day and got cancelled due to time limit allocated for the job on HPC. May I...
Hi dear developers, I have a question about the computation time of LJA. I'm actually trying to assemble a plant genome whose dimension should be around 500 Mbp. A previous...
In the context of the metagenomics work: I've noticed that, in the case where no reads are aligned to a contig, `samtools view` --> `samtools bam2fq` will produce an empty...
Hello! I have an issue during installation, could you please help me fix it? Thank you! ``` -- The CXX compiler identification is GNU 8.3.0 -- Check for working CXX...
Hi @AntonBankevich ? Is there need to purge haplotype duplication of the output assebmly ? As far as I know, Canu and HiFiasm needs another run of purge_dups. Thanks in...
Hi, this is kind-of related to issue #17. I've had an LJA assembly running for 18 days when our HPC went down. I'm wondering if LJA has functionality to restart...
