应用性能测试

$ module load arm/hifiasm/0.19.9
$ time hifiasm -o ath.asm -t 128 --ul CRR302667.fastq.gz --ul-cut 500 --h1 CRR302669_R1.fastq.gz --h2 CRR302669_R2.fastq.gz CRR302668.fastq.gz

$ module load arm/hifiasm/0.19.9
$ time hifiasm -o ath.asm -t 128  CRR302668.fastq.gz

$ module load arm/bwa/0.7.18 arm/samtools/1.21
$ bwa mem -t 128 -R '@RG\tID:test146\tPL:illumina\tLB:library\tSM:humen146' hg38.fa ERR194146_1.fastq.gz ERR194146_2.fastq.gz |samtools sort -@ 128 -o $ERR194146_srt.bam"

$ module load  arm/hisat/2.1.0 arm/samtools/1.21
$ time hisat2 -p ${thread} -x genome -1 sample_1.fq.gz -2 sample_2.fq.gz | samtools sort -@${thread} -o sample.sorted.bam

$ module load arm/gatk/4.6.0.0
$ gatk HaplotypeCaller --native-pair-hmm-threads $thread -R hg38.fa -L chr20 -I ERR194146_sort_redup.bam -O ERR194146_chr20_arm.vcf.gz

$ module load arm/vg/1.60.0
$ time vg giraffe -p -t $thread -Z ref.giraffe.gbz -d ref.dist -m ref.min -f sampleid_clean_1.fq.gz -f sampleid_clean_2.fq.gz > sampleid.gam

$ module load  arm/star/2.7.11b arm/samtools/1.21
$ STAR     --genomeDir star_index/      --runThreadN 128    --readFilesIn CRR232282_f1.fastq.gz CRR232282_r2.fastq.gz     --readFilesCommand zcat     --outFileNamePrefix CRR232282     --outSAMtype BAM SortedByCoordinate     --outBAMsortingThreadN $128

$ module load arm/megahit/1.2.9
$ megahit -1 sampleid_clean_R1.fq.gz -2 sampleid_clean_R2.fq.gz -o out  --presets meta-large --no-mercy --kmin-1pass -t 128

$ module load arm/minimap2/2.28  arm/samtools/1.21 
$ minimap2 -ax map-pb -t 128 MH63.fa MH63WGS_all_subreads.fasta.gz |samtools sort -@128 -o MH63WGS_all_subreads.bam