Jianshu_Zhao

The solution for now is, in sketch directory, sketch_schem, mod.rs, line: impl Default for SketchParams { fn default() -> Self { SketchParams::Mash { kmers_to_sketch: 10000, final_size: 1000, no_strict: false, kmer_length:...

Hello Ben, It has been a long time since my last message. Just want to make sure that the suggestions above make sense to you. Bindash is by far the...

Hi Team, GSearch is out! It can search GTDB or entire Refseq/IMG_VR in almost no time! and the running time does not grow with increasing number of genomes! https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae609/7714450 I...

Or at lease the bam file read and iterating bam files can be much faster. I noticed that there are some iterator implemented specifically for coverage taker. Thanks, Jianshu

Hello Ben, I check the rust-htslib and found that yes, reading bam file is sequential and that internal point cannot be share between threads because of the C language it...

Hi All, Thanks for letting me know dirseq @rhysnewell, I have being using it for a while for checking DNA contamination for RNA seq data (and Compare it with our...

Hello Ben, I want to bring this out again that calculating coverage of genes on a contig can be useful in some user cases I ran into. Essentially we just...

Hello Elaina, I am also doing similar work for recruitment plot. (reads mapped position, identity et.al. for plotting). Can we work together? Also see our way of calculating trimmed_mean, we...

Hello Team, Do you have this error when compiling or can you please provide a binary? Thanks, Jianshu

Hello Malfoy, I am actually comparing it with MASH, in which kmer size 21 is recommended for metagenomes while 16 for genomes (21 also works), very large kmer like 31...