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dnbaker
Fast and accurate genomic distances using HyperLogLog
Hi Is it possible to concatenate multiple premade sketches and then search against them in a single search? something along these lines ``` dashing sketch *.fasta cat *.hll > combined.hll...
Hello I have paired end reads from metagenomic libraries, ahead to estimate distances between these read sets should I concatenate the fastq files and then apply dist command? this is...
Hi, I was trying to use Dashing (Dashing version: v0.5.7b, downloaded May 2021) to estimate similarities between metagenomic assemblies (ie. each sample was represented by a set of Metaspades scaffolds)....
I'm looking for a method that can say whether an assembly is prokaryotic or eukaryotic. Was thinking this software might be helpful. Do you have any preconfigured databases that have...
Firstly, thanks a lot for your excellent tool! It's really cool! This is my question: Currently, I have three files, A.fq, B.fa, C.fa. And I want to calculate the distance...
Hi all, the make command fails after cloning with this error: bonsai/include/bonsai/entropy.h:2:10: fatal error: hll/circularqueue/cq.h: No such file or directory 2 | #include "hll/circularqueue/cq.h" So what is missing here? Thanks...
Can you create a dendrogram from the dist results? Also, could you recommend parameters for large fungal genome comparison?
When running dashing dist with 400,000 genomes the program succeeds when asking for csv "-T" output, but crashes when asking for binary "-b" output. Both commands succeed without problem when...
Is it possible to create a sketch using fastas streamed through a pipe to dashing? I'm manipulating both assembled genomes and k-mers and would like to compare them in the...
Is there a way of reading the binary distance matrix from "dashing cmp -b" directly into numpy?