Jianshu_Zhao
Jianshu_Zhao
Hello Daniel, For nt Jaccard distance, estimated by either MinHash (e.g. probminhash) , we can follow the MASH paper to do a log function transformation (-1/k*(2log(J)/(log(J)+1))) to approximate ANI, what...
Hello Daniel, I compute sketches using dashing2 sketch and store sketch using - - outfile. There is a sketch and a sketch.name.txt. But I am not sure how to feed...
Hello Daniel, I saw some avx to neon support here: https://github.com/kunpengcompute/AvxToNeon https://github.com/DLTcollab/sse2neon I did not check the exact types used for dashing2 but it seems it has included major types....
Hello Danial, I am comparing 100 metagenomes, total size about 1 TB, I assigned 2Tb memory but I always have the follow error after a few hours: #Calling Dashing2 version...
Hell Dashing2 developer, Dashing can be use for genome derelication in nt format but I am wondering wither it is an option to have it also work for amino acid...
Hello Kristoffer, There is a situation where reads are mapped to very close references (e.g., reference sequences are 90% or more similar to each other). For example, a bacterial community...
Dear StrobeAlign, I cannot compile it on a M1 pro chip (ARM), something like -O3 -march=armv8. Any possibilities to also provide a binary? THanks, Jianshu
Hello Kristoffer, I saw an interesting reimplementation of BWA-MEM Using MPI (Message Passing Interface) here: https://github.com/bioinfo-pf-curie/mpiBWA It seems a multi-node solution is becoming more appealing these days because most research...
Hello Team, IT seems not work on MacOS, cpu info is only GEnuineIntel (intel core i7) or nothing (ARM64) Any idea? Thanks, Jianshu
Actually it uses only 4-6 cores in real datasets no matter how many threads I assigned. Why limiting it to 16 cores only? How can I use 128 threads on...