要使用SIMDe编译,使用make -f Makefile.simde。要为ARM CPU编译,请使用上面给出的与ARM相关的命令行和Makefile.simde。 一般用法 不加任何选项时,minimap2以参考数据库和查询序列文件为输入,生成近似映射(即坐标仅是近似值,输出中没有CIGAR),以PAF格式呈现: minimap2 ref.fa query.fq > approx-mapping.paf ...
这里是分染色体的,我就只尝试一号染色体了 ~/biotools/software.package/bcftools-1.17/bcftools mpileup -f C24.fa --threads 16 -r chr1 -o Cvi.chr1.vcf -A -O v Cvi_C24.bam ~/biotools/software.package/bcftools-1.17/bcftools mpileup -f C24.fa --threads 16 -r chr1 -o Kyo.chr1.vcf -A ...
Common options: --logfile LOGFILE Path to the log file. If not specified, messages will only be written to the standard error output. (default: None) --tmp-dir TMP_DIR Full path to the directory where temporary files will be stored. ...
Do not delete the directory storing temporary files after completion. --no-seccomp-override Do not override seccomp options for docker (default: None). --version View compatible software versions. GPU options: --num-gpus NUM_GPUS Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) wi...
bgzip-f-@16chr1.vcf tabix chr1.vcf.gz 对数据进行过滤 代码语言:javascript 代码运行次数:0 运行 AI代码解释 ~/biotools/software.package/bcftools-1.17/bcftools view-e'GT[*]="mis"'chr1.vcf.gz>chr1.nomissing.vcf~/biotools/software.package/bcftools-1.17/bcftools view-e'GT[*]="het"'chr1.no...
Minimap2是知名比对工具BWA的开发者Li Heng新开发的比对工具,它能够快速的将DNA或者mRNA序列比对到参考基因组上,使用场景有下面几种: 将PacBio或OXford Nanopore的read和已有参考基因组(如人类)进行比对 寻找高错误率read(15%)之间的overlap 将PacBio Iso-Seq 或Nanopore cDNA或RNA序列比对到参考基因组 将illumina ...
Minimap2 can useSIMD Everywhere (SIMDe)library for porting implementation to the different SIMD instruction sets. To compile using SIMDe, usemake -f Makefile.simde. To compile for ARM CPUs, useMakefile.simdewith the ARM related command lines given above. ...
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Mapping options -f FLOAT|INT1[,INT2] If fraction, ignore top FLOAT fraction of most frequent minimizers [0.0002]. If integer, ignore minimizers occuring more than INT1 times. INT2 is only effective in the --sr or -xsr mode, which sets the threshold for a second round of seeding. -...
Minimap2 is a general-purpose mapper to align long noisy DNA sequences against a large reference database. It targets query sequences of 1kb-100Mb in length with per-base divergence typically below 25%. Minimap2 is ~30 times faster than many mainstream long-read aligners and achieves higher...