Jianshu_Zhao

ARM compiling error

4

Hello hifiasm team, Compiling on macOS ARM has the following error: g++ -c -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall CommandLines.cpp -o CommandLines.o g++ -c -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall...

-max_target_seqs 1 is not guaranteed to find the best hit in the database even in -task blastn mode

3

#### Summary: Line 434-439 in anib.py, blastn options -max_target_seqs 1 is not guaranteed to find the best hit in the database even in -task blastn mode #### Description: Database search...

mash pre-cluster sketch size?

5

Dear dRep team, This is confusing to me when using mash sketch size 1000: def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folder, logdir, **kwargs): dry = kwargs.get('dry', False) p = kwargs.get('processors', 6) MASH_s...

How to add classification for each genome in the html heatmap

3

Hello, I am wondering how to add classification information for each genome like in the NAR paper in the html heatmap output. Thanks, Jianshu

hmmsearch not parallelized

3

dear DRAM team, I found that the hmmsearch is really slow and ran just in 2 threads but I have 200 genomes to search. Would that be possible to make...

A beautiful Rust implementation. I have run benchmarks for various dataset with very good performance and recall. More metric distance are supported including hamming, Hellinger distance, Jensen-Shannon distance between probability...

question on Choosing M and dataset type

4

Hello Team, I am wondering how to choose the M for starters or with a new dataset that has never been studied. Just randomly choosing one between 16 and 64...

Question--time complexity for high LID dataset

1

Hello hnswlib Team, I am wondering for high Local Intrinsic dimension dataset, complexity for database building is still O(N*log(N))? Another question I have is, from a HNSW graph structure, we...

multi-node parallel hnsw

7

Dear team, This is a question on whether we can parallel hnsw on different computing node (so distributed memory) but not just on one node. If not, I split my...

This command only support for usearch5 by default, which is old and not so useful. Can you please help with it (I do not like qiime2 because I do not...