This website is a virtual proof that I'm awesome https://daylily-informatics.github.io/ with bwa mem2 meme - An experiment looking into the effects on mapping statistics and SNV calling with bwa kmer -k sizes 16-23. Conclusions SNV Calling The effect of altering bwa mem2 meme kmer -k sizes has neglible effects on calling all classes of SNVs (SNPts, SNPtv, INS, DEL, Indel), with a small gain seen... Mon, 08 May 2023 00:00:00 -0700 https://daylily-informatics.github.io/2023-05-08-snv-calling-performance-by-bwa-kmer.md/ https://daylily-informatics.github.io/2023-05-08-snv-calling-performance-by-bwa-kmer.md/ The beginning of the Daylily Informatics Blog. - Introducing The Daylily Multi-Omic Analysis Framework: 30x WGS Pipelines Running < 1hr, for dollars a sample & achieving Fscores of up to 0.998. Daylily daylily is an analysis framework which automates everything from AWS compute resource generation and management through running various WGS pipelines and tools. It is highly configurable,... Mon, 08 May 2023 00:00:00 -0700 https://daylily-informatics.github.io/2023-05-08-rapid-wgs-fastq-to-snv-vcf-pipeline/ https://daylily-informatics.github.io/2023-05-08-rapid-wgs-fastq-to-snv-vcf-pipeline/ The beginning of the Daylily Informatics Blog. - I would like to share a combination of techniques which produce an aligned+sorted+indexed bam in 34m for $1.89 BWA-MEM2meme Here is the entire bwa-meme command which daylily executes the following on a 128 vcpu instance: JEMALLOC_CONF='oversize_threshold:1024,background_thread:true,huge:true,huge_page:1G,arena_max:4' \ LD_PRELOAD=resources/lib/libjemalloc.so.1 \ resources/numa/numactl \ --cpunodebind=0,1 \ --membind=0,1 \ bwa-meme mem \ -R '@RG\tID:RIH0A0\tSM:RIH0A022\tLB:NoAmpWGS\tPL:ILMN\tPU:CombinedLanes\tCN:CenterName\tPG:bwamem2meme'... Wed, 03 May 2023 00:00:00 -0700 https://daylily-informatics.github.io/2023-05-03-very-fast-bwa-mem2ert-invocation/ https://daylily-informatics.github.io/2023-05-03-very-fast-bwa-mem2ert-invocation/