Jianshu_Zhao

Hello Daniel, Do you have the dashing2 paper preprint ready? I would be very happy to read it. Thanks, Jianshu

Hello Daniel, I come back to this after a few tries. I realized that for genome assemblies, especially for those assembled from metagenomes (a lot of genomes species for metagenomes),...

Hello Daniel, I am also sorry for late response, and congrats! Dr. Baker! A few questions related to Minhash, weighted minhash, probminhash and contamination minhash: when comparing MinHash (mash software)...

I have a different error when running pip install MulticoreRSNE: Building wheel for MulticoreTSNE (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/homebrew/opt/[email protected]/bin/python3.9 -u -c 'import...

Hello Kristoffer, Yes, there can be so many reference sequences. When we do sequencing of a lot of cells, like so many species in fresh water samples, coverage will always...

Hi Check this on M1: Jianshus-MBP-2:StrobeAlign jianshuzhao$ g++ -std=c++14 main.cpp source/index.cpp source/ksw2_extz2_sse.c -lz -fopenmp -o StrobeAlign -O3 -march=armv8.5-a Undefined symbols for architecture arm64: "_ksw_extz2_sse", referenced from: __Z9ksw_alignPKciS0_iiiiiR10ksw_extz_t in ccdGVhMg.o ld:...

Hello @ksahlin , See below: g++ -std=c++14 main.cpp source/index.cpp source/xxhash.c source/ssw_cpp.cpp source/ssw.c source/pc.cpp source/aln.cpp -lz -lpthread -o strobealign -O3 -march=armv8.4-a In file included from source/ssw_cpp.cpp:6: source/ssw.h:17:10: fatal error: emmintrin.h: No...

You will love it! Everything is 3-5 times faster than an intel version, BWA-MEM neon version is 3.5 faster than an intel avx2 version on average. I believe strobealign will...

(ERR): bowtie2-align died with signal 11 (SEGV) Still this bug in 2.4.3 Jianshu

Hello Team, I did not expect this but from v 2.3 to v2.4.5.1 this happens all the time: Jianshus-MBP-2:test_data jianshuzhao$ bowtie2 -x ./all_mag.fasta -f --interleaved ./T4AerOil_sbsmpl5.fa.gz -S all_mag_bowtie2.sam --threads 4...