雖然這篇bwa-mem2鄉民發文沒有被收入到精華區：在bwa-mem2這個話題中，我們另外找到其它相關的精選爆讚文章
[爆卦]bwa-mem2是什麼？優點缺點精華區懶人包
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#1bwa-mem2/bwa-mem2: The next version of bwa-mem - GitHub
Bwa -mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset ...
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#2BWA-MEM2 Review: Should You Upgrade? - Inside DNAnexus
The Burrow-Wheeler Aligner (BWA-MEM), which requires no introduction, is one of the most popular software tools in the Bioinformatics and ...
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#3Alignment using bwa-mem2 - Biostars
Should be enough. Be sure that if you are using a job scheduler you actually allocated this memory (in SLURM that would be the --mem ...
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#4bwa-mem2 on Biowulf - NIH HPC
Bwa -mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on ...
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#5bwa mem2 · Wiki · Arm HPC Resources / packages - GitLab
Lifesciences; The Burrow-Wheeler Aligner (BWA-MEM) is frequently used in the Bioinformatics and Genomics industry to generate alignments to ...
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#6生信软件的使用:bwa-mem2小测试 - 简书
生信软件的使用:bwa-mem2小测试. blue_unique 关注. 2020.06.09 06:00:39 字数516阅读2,736. 写在前面. 最近在利用小麦的重测序数据进行mapping，小麦是一个很奇特的 ...
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#7Bwa Mem2 - :: Anaconda.org
conda install. linux-64 v2.2.1. To install this package with conda run: conda install -c bioconda bwa-mem2. Description. By data scientists, for data ...
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#8Accelerated Seeding for Genome Sequence Alignment with ...
Abstract: Read alignment is a time-consuming step in genome sequencing analysis. The most widely used software for read alignment, BWA-MEM, and the recently ...
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#9BWA-MEM2 - Snakemake Wrappers
Bwa -mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, ...
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#10Bwa-mem2 - 健康貼文懶人包
提供Bwa-mem2相關文章，想要了解更多Bwa 0.7 7、aligning sequence reads clone sequences and assembly contigs with bwa-mem、BWA MEM tutorial相關社群資訊或書籍， ...
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#11Manual Reference Pages - bwa (1)
The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for ...
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#12BWA-MEM2 - UFRC Help and Documentation
Description. bwa-mem2 website. We are happy to announce that the index size on disk is down by 8 times and in memory by 4 times due to ...
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#13BWA-MEM emulated with a machine learning approach
Our evaluation shows that BWA-MEME achieves up to 3.45x speedup in seeding throughput over BWA-MEM2 by reducing the number of instructions ...
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#14(PDF) BWA-MEME: BWA-MEM emulated with a machine ...
Our evaluation shows that BWA-MEME achieves up to 3.45x speedup in seeding throughput over BWA-MEM2 by reducing the number of instructions ...
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#15Tryping pipe output to samblaster from bwa-mem2 - Stack ...
I am trying to upgrade my workflow from bwa to bwa-mem2. This command usually works. /usr/local/bin/bwa mem -K 100000000 -t 4 -Y -R ...
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#16Sanchit Misra on Twitter: "We have released bwa-mem2 v2.1 ...
We have released bwa-mem2 v2.1 in which we address the main feedback that index of the reference was too big. The index size on disk is down by 8x and in ...
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#18bwa-mem2 - Bountysource
Executing in AVX512 mode. Command: ⟫ bwa-mem2 mem -t 8 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/ERR3242672_1.fastq.gz / ...
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#19Bwa-mem2 - macでインフォマティクス
Bwa -mem2はbwaのbwa-memアルゴリズムのネクストバージョンである。bwaと同じアラインメントを生成し、データセット、実行中のマシンに依存し ...
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#20Running bwa vs bwa-mem2 - Oyat consulting
bwa -mem2 needs 9 times more memory: 51,5GB while bwa needs 5.7GB. While bwa runs fine on a solid laptop, bwa-mem2 will not run on an average ...
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#22Taipei Bioinformatics Omnibus (北-BiO) | BWA-MEM2 v2.0 ...
This is the first production release of BWA-MEM2. Changes since the last release: Made the source code more secure with more than 300 changes all across it.
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#23Package Recipe 'bwa-mem2' — Bioconda documentation
recipe bwa-mem2. The next version of bwa-mem. Homepage. https://github.com/bwa-mem2/bwa-mem2. License. MIT. Recipe. /bwa-mem2/meta.yaml. Links. doi: 10.1109/ ...
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#24BWA MEM for single or paired-end reads and own genome
When performing the Smith-Waterman extension of the seed alignments, BWA-MEM keeps track of the best score reaching the end of the read. If this score is larger ...
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#25BWA-MEM - Unipro UGENE User Manual - WIKI
BWA is a fast light-weighted tool that aligns relatively short reads to a reference sequence. Click this link to open BWA homepage. BWA-MEM ...
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#26Efficient Architecture-Aware Acceleration of BWA-MEM for ...
BWA -MEM is one of the most widely used tools for sequence mapping and has tens of thousands of users. In this work, we focus on accelerating BWA ...
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#27HPC + Science
BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences ... BWA-mem2 is the next version of the bwa-mem algorithm in bwa.
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#28bwa mem 比对分值参数测试_sinat_32872729的博客
command 对应的多种命令，这里使用的是 mem ，即使用BWA-MEM算法进行序列比对。 bwa mem 命令比对： 下方官网上介绍的mem命令： 在这里插入图片描述.
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#29bwa-mem2 - 程序员秘密
输出应与原始的bwa-mem版本0.7.17相匹配。 从提交e0ac59e开始，我们有一个git子模块safestringlib。 要获得它，请在克隆时使用--recursive或在已克隆的存储库中使用“ ...
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#30AUR (en) - bwa-mem2-git - Arch Linux
Description: The next version of Burrows-Wheeler Aligner MEM algorithm. Upstream URL: https://github.com/bwa-mem2/bwa-mem2. Licenses: custom.
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#31BWA Aligner - Illumina
Align samples with the BWA-MEM aligner to a reference genome, including custom references created from imported FASTA files.
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#32BWA-MEM2 alignment-Snakemake - Bioinformatics Stack ...
Looking to launch executable "/scicore/home/cichon/GROUP/test_workflow/.snakemake/conda/0ecf6ba401c70d7501c73bb1c733a060/bin/bwa-mem2.avx", ...
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#33bwa 使用指南#1. 介紹#2. 安裝#3. 使用示例#4. 常用命令行#5 ...
對於70-100bp Illumina讀數，BWA-MEM也比BWA-backtrack有更好的性能。 對於所有的算法，BWA首先需要爲參考基因組構建fm-index(index 命令)。使用不同的子 ...
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#34dceoy/bwa-mem2 - Docker Image
Images on Docker Hub: abra2 · alfred · ascat · bamsnap · bcftools · bedops · bedtools · bioconda · bowtie2 · bwa · bwa-mem2 · cufflinks · cnvkit ...
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#35tomaskopsa/bwa-mem2 - githubhot
Added MC flag in the output sam file in commit a591e22. Output should match original bwa-mem version 0.7.17. As of commit e0ac59e, we have a git submodule ...
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#36b4a22d90cce9 - Galaxy | Tool Shed
Bwa -mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,
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#37BWA-MEM2-IPDPS 2019 - SlideShare
Slightly modified version of slides on BWA-MEM2 that I presented at IPDPS'19 for the paper: Efficient Architecture-Aware Acceleration of BWA-MEM for ...
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#38BWA-MEM
BWA is a reference genome assisted assembler for read data. It maps reads to a given reference genomes. BWA contains several algorithms, SeqSphere+ supports ...
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#39Additional evaluations show that specific BWA‐aln settings ...
Xu et al. (2021) recently recommended a new parameterization of BWA-mem as a superior alternative to the widely-used BWA-aln algorithm to ...
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#40IMPROVING BWA-MEM WITH GPU PARALLEL COMPUTING
BWA -MEM is an important part of the BWA software package for sequence mapping. Because of its high speed and accuracy, we choose to parallelize the popular ...
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#41BWA-MEM built-in genome(s) - usegalaxy.eu support - Galaxy ...
Hello everyone, I'm using galaxy to trim and align data from targeted DNA-seq. Using BWA-MEM I've seen that between built-in genomes there is not the hg38 ...
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#42Issues · bwa-mem2/bwa-mem2 - GitHub
The next version of bwa-mem . Contribute to bwa-mem2/bwa-mem2 development by creating an account on GitHub.
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#43Running BWA Commands - Holland Computing Center
The bwa mem algorithm is one of the three algorithms provided by BWA. ... reference genome generated from bwa index, and input_reads.fastq, ...
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#44High Percentage of Soft Clipping, BWA-MEM, MiSeq
Member. Location: California. Join Date: Jan 2012. Posts: 11. Default High Percentage of Soft Clipping, BWA-MEM, MiSeq ...
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#45bwa-mem中的ksw演算法到底是怎麼回事兒？ - IT閱讀
研究了這麼久bwa-mem演算法，也不知一次啃了ksw這塊硬骨頭，之前沒有好好總結，今天來重點研究一下它。 主要研究的物件是ksw_extend2函式，它是一個單 ...
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#46bioconductor package for BWA-MEM ?
I was wondering if there is a R/Bioconductor package that can run BWA-mem alignment (just like how RSamtools is the Bioconductor implementation of Samtools) ...
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#47GATK流程不用再分割小麦染色体part2-马省伟的博文 - 科学
具体请参见https://github.com/Genetalks/gtz#bwa-mem2。如果fastq文件使用普通的gz格式压缩，那就使用正常的bwa-mem就可以。 关于genome intervals文件， ...
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#48[PDF] Heterogeneous hardware/software acceleration of the ...
This paper presents an accelerated version of BWA-MEM, one of the most popular read alignment algorithms, by implementing a heterogeneous ...
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#49BwaMemIndexImageCreator - GATK
Tools that utilize BWA-MEM (e.g. BwaSpark, PathSeqBwaSpark) require an index image file of the reference sequences.
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#50Improving Computational Methods for High-throughput ...
Project. BWA. With the release of BWA-MEM2, this work will continue to maintain and improve BWA, and add the ARM64 support ...
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#51bwa-mem2 - Debian Med
bwa -mem2. Project ID: 37227. Star 0 · 45 Commits · 3 Branches · 4 Tags · 788 KB Files · 788 KB Storage. Debian packaging for bwa-mem2.
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#52Global-Scale Scientific Cloud Computing with Kubernetes and ...
This is done with a tool called bwa-mem2. This means we want our Kubernetes-based pipeline to execute two FastQC containers on a pair of ...
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#53BWA-MEM vs Minimap2: WGS somatic variant calling
We evaluate differences between bwa-mem and minimap2-aligned reads for somatic variant calling.
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#54SeedEx: A Genome Sequencing Accelerator for Optimal ...
This is the key seed extension kernel in the mainstream aligners, including BWA-MEM and BWA-MEM2. SeedEx targets the semi-global and global ...
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#55WES/WGS数据比对，除了bwa mem，还有哪些可替代方案
bwa mem 性能较好、可靠稳定，一直是WES/WGS数据分析的首选比对工具，随着技术的发展，有了越来越多的可替代方案。
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#56生物信息学 - 上海科技大学
bwa. 0.7.17. X86_64,. ARM. https://opensource.org/licenses/GPL-3.0 ; BWA-MEM2. 2. X86_64. https://opensource.org/licenses/MIT ; Wtdbg2. 2.5. ARM.
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#58Browse Dataset Files - European Genome-Phenome Archive
Browse Dataset Files. ICGC PCAWG Dataset: LIRI-JP PCAWG WGS BWA ... ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: LIRI-JP.
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#59An Efficient GPUAccelerated Implementation of Genomic ...
BWA -MEM is the de-facto industry-standard for the mapping stage. ... Hardware/Software Acceleration of the BWA-MEM DNA Alignment Algorithm.
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#60Gatk4 Cnv gatk4 cnv. map with bwa mem, mark duplicates ...
gatk4 cnv. map with bwa mem, mark duplicates ecetera I haven't done that in a while but back then it was like a few commands. Just as NGS technologies have ...
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#61Evaluation of Genome Alignment Workflows on HPC Processors
BWA -MEM2 is a well-known sequence alignment application. As a second contribution, we port. BWA-MEM2 from x86 64 to Armv8 with SVE.
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#63下一个版本的bwa-mem - wenyanet
(The next version of bwa-mem ). Created at: 2019-02-26 23:00:44. Language: C++. URL: https://github.com/bwa-mem2/bwa-mem2. License: NOASSERTION.
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#64Standard error of bwa-mem2 output contained non-ASCII #146
Dear bwa-mem2 developers,. I am facing a problem with the generated log file after mapping with bwa-mem2 mem command. In the output to standard error, ...
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#65PipeMEM: A Framework to Speed Up BWA-MEM in Spark with ...
(1) Background: DNA sequence alignment process is an essential step in genome analysis. BWA-MEM has been a prevalent single-node tool in genome alignment ...
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#66BWA MEM算法 - 博客园
现在BWA大家基本上只用其mem算法了，无论是二代还是三代比对到参考基因组上，BWA应用得最多的就是在重测序方面。 Aligning sequence reads, clone ...
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#67how to extract mapped reads from output of BWA-MEM to a ...
By default, BWA-MEM on the main galaxy server does not seem to give an option to write the mapped or unmapped reads in an alignment run to ...
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#68bwa的使用 - 陈连福的生信博客
BWA-bactrack: 用于进行Illumina reads 的比对。reads 的长度最大为100bp。 ... bwa mem genome reads.fq > aln-se.sam $ bwa mem genome read1.fq ...
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#69BWA-MEM 不同方法的Mapping 结果比较| GeneDock 文档
总结：BWA-MEM 并不是每条read 输出一个Mapping 结果，因为存在chimeric alignments，所以有的会有多条。 二、不同线程数Mapping 对结果的影响. $ wc -l ...
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#70Qiime2 Fastq qiime2 fastq. 2) Here we walk through version 1 ...
Qiime2 artifacts are structured compressed archives containing a dataset (e. So far: I used BWA mem to convert them to Sam file. Lukman, bisa gan caranya abis ...
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#71Feature request: add `bwa mem2` support - Giters
It seems that bwa-mem2 is much faster. ... fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome.
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#72Gatk4 Cnv gatk4 cnv. 6806-810A>G and c. For CNV prediction ...
... and navigating to the. map with bwa mem, mark duplicates ecetera I haven't done that in a while but back then it was like a few commands.
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#73Molecular parallelism in signaling function across different ...
We aligned paired and trimmed reads to the common yellowthroat reference genome using bwa mem with default settings (v0.7.17; ...
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#74Spatio-temporal dynamics of intra-host variability in SARS ...
... out using SAMtools (21) and mapped to the SARS-CoV-2 reference genome (NC_045512.2) using Burrows-Wheeler Aligner (BWA-MEM) (22).
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#75Molecular characterization of methicillin-resistant ... - Nature
... genome (ASM964v1, GenBank accession: BA000018.3) using Burrows-Wheeler Aligner (BWA) version 0.7.17 with the BWA-MEM algorithm.
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#76Phylogeography and transmission of M. tuberculosis in Moldova
... FastQC [11] and mapped to the H37Rv reference strain (NC_000962.3) using BWA “mem” [12] and sorted with SAMtools v.1.10 [13] (S1 Data).
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#77Gatk4 Cnv gatk4 cnv. This pipeline calls germline copy ...
It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. Stand-up & Jokes. Workflows for somatic copy number variant discovery with GATK4. 3 ...
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#78bwa-mem2 is a popular open source software
bwa -mem2 is a popular opensource software developed by bwa-mem2 in C++ having 487 stars .bwa-mem2is related to bioinformatics c-plus-plus genomics topics.