我们很高兴地宣布,由于仅使用一种类型的FM索引(2bit.64而不是2bit.64和8bit.32)和8x压缩,因此磁盘上的索引大小减少了8倍,内存中的索引大小减少了4倍后缀数组。 例如,对于人类基因组,磁盘上的索引大小从〜80GB降低到〜10GB,而内存占用从〜40GB降低到〜10GB。 由于减少了索引IO时间,因此对读取映射几乎没...
bwa-mem2是指令集优化版bwa mem,它产生与bwa相同的对齐,并且速度约为1.3-3.1倍,具体取决于用例、数据集和运行机器,近期的版本极大降低了内存和存储使用量(使用了FM-index,和 8x compression) 最初的bwa是由李恒开发的. bwa-mem2的性能增强主要由英特尔并行计算实验室的Vasimuddin Md(@yuk12)和Sanchit Misra(@s...
运行速度第二个很快,大约8个小时的时间,bwa-mem2可以得到50G的比对结果,而bwa的结果是5.7Gb,真的是超级快了. 但是也存在一些问题,那就是在投任务的时候,bwa-mem2的第二个任务被kill了,看了一下报错结果,显示segmentation fault。但是使用bwa就不存在这个问题,个人更倾向于该版本的问题,但是还没有很好的解决方法。
Download SRA toolkit fromhttps://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software#header-global tar xfzv sratoolkit.2.10.5-centos_linux64.tar.gz Download D2: sratoolkit.2.10.5-centos_linux64/bin/fastq-dump --split-files SRR7733443 ...
天盼夜盼,Bwa-mem2 正式版终于发布了 这个是版本发布的截图 看下这个软件的对应的文章 Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems 摘要如下: Abstract: Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very ...
首先是bwa2的安装，貌似现在不能使用conda安装，官网给了详细的介绍，我捡重点的给大家看一下 官网介绍 GitHub - bwa-mem2/bwa-mem2: The next version of bwa-mem (WIP; not recommended for production uses at the moment)重点内容 两种安装方法 对参考基因组建立索引 一共生成了7个文件，其中...
#minimap2 baseline docker run -v $PWD/test:/test mm2-fast:latest /baseline/minimap2 -ax map-ont /test/MT-human.fa /test/MT-orang.fa > minimap2_baseline #mm2-fast docker run -v $PWD/test:/test mm2-fast:latest /mm2fast/minimap2 -ax map-ont /test/MT-human.fa /test/MT-orang.fa...
Where are the differences from? ALT contigs. For all samples, around half of the differences are either exclusively classified by BWA-MEM or BWA-MEM2. The other half of differences were classified by BWA-MEM reporting all alternative mapping locations (while BWA-MEM2 does not report any of ...
bwa-mem2 is out and it should 80% faster than bwa-mem. Wow! https://github.com/bwa-mem2/bwa-mem2
These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ...