雖然這篇Samtools鄉民發文沒有被收入到精華區：在Samtools這個話題中，我們另外找到其它相關的精選爆讚文章
[爆卦]Samtools是什麼？優點缺點精華區懶人包
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#1Samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: ... Samtools and BCFtools both ...
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#2samtools [生物資訊實驗室]
Samtools 是處理Alignment軟體產生出SAM檔之工具組，包含以下小程式. Usage: samtools <command> [options] Command: view SAM<->BAM conversion sort sort alignment ...
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#3Samtools - GitHub
samtools · htslib: C-library for handling high-throughput sequencing data · samtools: mpileup and other tools for handling SAM, BAM, CRAM · bcftools: calling and ...
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#4samtools使用大全- IT閱讀
samtools 是一個用於操作sam和bam檔案（通常是短序列比對工具如bwa,bowtie2,hisat2,tophat2等等產生的，具體格式可以在訊息框輸入“SAM”檢視）的工具 ...
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#5SAMtools
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: ... SAM Tools provide ...
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#6samtools - 我們的基因體時代Our "Gene"ration
在position-sorted和indexed過的bam file，我們可以擷取特定區域的alignment狀況使用samtools view這指令。 首先，先將想要使用的bam file用 ...
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#7SAMtools - Wikipedia
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary ...
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#9SAMtools - an overview | ScienceDirect Topics
SAMtools. SAMtools [20] – SAM (Sequence Alignment/Map) tools are a set of utilities that can manipulate alignments from files in the BAM format, ...
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#10samtools使用方法參數整理 - 台部落
samtools 的說明文檔：http://samtools.sourceforge.net/samtools.shtml samtools是一個用於操作sam和bam文件的工具合集。包含有許多命令。
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#11Dave's Wiki | SAMTools
SAMTools provides various tools for manipulating alignments in the SAM/BAM format. The SAM (Sequence Alignment/Map) format (BAM is just the binary form of ...
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#12Samtools – ENCODE - Encodeproject.org
Samtools is a suite of programs for interacting with high-throughput sequencing data. SAMtools implements various utilities for post-processing alignments in ...
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#13Sequence Alignment/Map Format Specification - Samtools
pdf at https://github.com/samtools/hts-specs. 9. Page 10. 2 Recommended Practice for the SAM Format. This ...
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#14SAMtools
SAMtools. SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in ...
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#15Subsampling Bam File With Samtools - Biostars
Subsampling not working for fractions above 50% is a known bug in samtools 0.1.18. (See [Samtools-help] Randomized Subsampling Bam File / Subsampling above ...
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#16SAMtools - bio.tools
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion ...
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#17Running SAMtools Commands - HCC-DOCS
SAMtools Index. The samtools index command creates a new index file that allows fast look-up of the data in a sorted SAM or BAM file.
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#18Samtools - conda install
To install this package with conda run one of the following: conda install -c bioconda samtools conda install -c bioconda/label/cf201901 samtools ...
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#19SAMtools - Docs CSC
SAMtools provides tools for using and manipulating SAM and BAM formatted alignments. You can use SAMtools for example for indexing, variant calling and ...
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#20Rsamtools - Bioconductor
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, ...
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#21Twelve years of SAMtools and BCFtools | GigaScience
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file ...
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#22samtools.txt - NERC Environmental Bioinformatics Centre ...
DESCRIPTION Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, ...
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#23samtools on Biowulf - NIH HPC
Samtools is a suite of applications for processing high throughput sequencing data: samtools is used for working with SAM, BAM, ...
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#24samtools(1) - Linux man page
Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, does .
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#25SAMtools的使用说明 - 简书
一、原理原文章：The Sequence alignment/map (SAM) format and SAMtools 摘要1、SAM格式是一种通用的，用于储存比对后的...
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#26Samtools - BioLib
Samtools Main samtools application Samtools is a set of utilities that manipulate alignments in the BAM/SAM/CRAM format. Commands For extensive description ...
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#27SAMtools - Sheffield HPC Documentation
http://www.htslib.org/doc/samtools.html. SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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#28SAMtools | PSC
SAMTools. SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments ...
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#29什么是SAMtools
SAMtools 是一组实用程序，用于与Heng Li编写的SAM，BAM和CRAM格式的短DNA序列读取比对进行交互并进行后处理。这些文件是由短读取对齐器（如BWA）作为 ...
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#30SAMtools - Metagenomics wiki
Note: SAMtools mpileup counts only primary aligned reads. SAMtools discards unmapped reads, secondary alignments and duplicates. To consider also secondary ...
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#31Install samtools on UNIX system - Easy Guides - Wiki - STHDA
Samtools is a useful tool for manipulating and visualizing .bam files. Installation. 1. Download the most current version from the Samtools website.
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#32Samtools-hybrid - Genome Analysis Wiki
This hybrid version of samtools is essentially samtools version 0.1.7a (r510), except the 0.1.7a bgzf logic and "calmd" functionality have been replaced with ...
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#33samtools | Advanced Research Computing at Virginia Tech
Introduction: SAMTOOLS is a set of tools for high throughput sequencing data. SAMTOOLS is associated with the SAM (Sequence Alignment/Map) format,
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#34SAMtools / BCFtools / HTSlib - Wellcome Sanger Institute
SAMtools, BCFtools. and HTSlib are tools for manipulating sequence alignment (SAM, BAM, CRAM) and variant call (VCF and BCF) files.
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#35SAMtools - HPC @ QMUL
SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, ...
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#36samtools (rrid:scr_002105) - SciCrunch | Research Resource ...
Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format.
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#37[samtools]merge命令简介_睿智如水 - CSDN博客
samtools merge命令的功能描述： 当有多个样本的bam文件时，可以使用samtools的merge命令将这些bam文件进行合并为一个bam文件。Merge命令将多个已经 ...
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#38Samtools安装及使用 - 生信菜鸟团
samtools view -bS tmp1.sam > tmp1.bam. samtools sort tmp1.bam tmp1.sorted ... samtools是一个用于操作sam和bam文件的工具合集。包含有许多命令。
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#39SAMtools - Pasteur.fr
This will create a file named sorted.bam.bai which contains the index. Example: samtools view file.sam >file.bam samtools sort file.bam -o file_sorted.bam.
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#40Samtools: viewing, counting and sorting your alignment data
Introduction to Samtools - manipulating and filtering bam files. As we showed you yesterday, the main type of output from aligning reads to ...
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#41biocontainers/samtools - Docker Image
biocontainers/samtools. By biocontainers • Updated 2 years ago. Tools for manipulating next-generation sequencing data. Container. OverviewTags.
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#42Details of package samtools in sid
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM ...
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#43Sequences and Genomic Features 7: SAMtools I - Week Two
Video created by Johns Hopkins University for the course "Command Line Tools for Genomic Data Science". In this module, we'll be taking a ...
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#44samtools升级至1.3 | GeneDock 文档
Usage: samtools <command> [options] Commands: -- Indexing dict create a sequence dictionary file faidx index/extract FASTA index index ...
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#45Samtools - UFRC Help and Documentation
Description. samtools website. SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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#46Understanding and manipulating SAM/BAM alignment files
We will also discuss samtools, which is a free software package for manipulating SAM/BAM files. Understanding how to use samtools is important since BAM ...
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#47Binding to the C samtools library - Hackage
Binding to the C samtools library, which reads and writes SAM format alignments, both binary and tab- delimited text formats.
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#48SAMtools | SCAI - HPC Cineca
SAMtools. Version: 1.3.1 (MARCONI) 1.12(GALILEO). SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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#49HPC Grid Tutorial: How to Use SAMtools - Articles
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence ...
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#50Newest 'samtools' Questions - Bioinformatics Stack Exchange
samtools. Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about ...
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#51Optimization of SAMtools sorting using OpenMP tasks
SAMtools is a widely-used genomics application for post-processing high-throughput sequence alignment data. Such sequence alignment data are ...
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#5232 questions with answers in SAMTOOLS | Science topic
I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server? I have used Samtools View. That is giving me some ...
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#53learning how to filter and manipulate with SAM/BAM files
Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) format, ...
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#54samtools小实例(未完成) - 云+社区
第三步：使用samtools将sam格式转换为bam格式并且把bam ... samtools index eg2.sorted.bam #过滤没有比对到参考基因组的reads samtools view -F 4 ...
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#55samtools使用方法總結 - 雪花台湾
view命令中，對sam文件頭部的輸入(-t或-T）和輸出(-h)是單獨的一些參數來控制的。 Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]
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#56SAMtools - RCDS
SAMtools. SAMtools is a set of tools for manipulating files in SAM (Sequence Alignment/Map) format. A typical application is to call variants based on ...
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#57SAMtools - SBGrid Consortium - Supported Software
SAMtools · Description. (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for ...
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#58SAMTools - Evolution and Genomics
SAMTools. SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:.
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#59SAMtools - HPC wiki
All versions of SAMtools installed on the PMACS HPC systems are now made available as modules. samtools v0.1.18 is available as a module : [ ...
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#60How To Install "samtools" Package on Ubuntu - ZoomAdmin.com
Samtools is a set of utilities that manipulate nucleotide sequence alignments in the binary BAM format. It imports from and exports to the ascii SAM (Sequence ...
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#61samtools - Homebrew Formulae
samtools. Install command: brew install samtools. Tools for manipulating next-generation sequencing data. https://www.htslib.org/. License: MIT.
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#62Manipulating SAM/BAM alignment files - Homer Software and ...
Understanding how to use samtools is important since BAM files are often the input files needed for many different analysis programs. Sometimes they need to be ...
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#63SAMtools – MetaCentrum
Description. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and ...
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#64linux下samtools安装指南- 组学大讲堂问答社区
samtools 是一个用于操作sam和bam文件的工具软件，能够对比对文件进行二进制查看、格式转换、排序及合并等，结合sam格式中的flag、tag等信息，还可以 ...
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#65[2012.10295] Twelve years of SAMtools and BCFtools - arXiv
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings
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#66操作SAM文件,就用Samtools工具集 - 知乎专栏
samtools 是一个用于操作sam和bam文件的工具合集，包含有许多命令。下面我们就来介绍一下使用Samtools操作SAM文件使用方法。 操作步骤samtools是一个用于操作sam和bam ...
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#67A Sample Software Installation – Samtools - FutureLearn
Finally, install Samtools by entering the command below. conda install -c bioconda samtools. Again proceed by typing y. Installing Samtools on Mac.
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#68使用BWA、GATK、Samtools软件进行基因测序 - 阿里云帮助文档
主要用于去除重复序列、重新校正碱基质量值、变异检查等。 Samtools是用于处理sam和bam格式的工具软件，能够查看二进制文件、转换文件格式、对文件排序及 ...
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#69The Sequence Alignment/Map format and SAMtools | Paper
SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus ...
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#70samtools工具的使用-测序原理-数据格式-数据库
1）samtools简介-背景：前面我们讲过sam/bam格式，sam文件虽然是可读的文本文件形式，但是...生信技能树.
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#71Samtools Introduction Version 0.1.19 General Tips
Samtools hardly needs an introduction, it is one of the cornerstones of bioinformatics processing and is at the heart of the business of sequence.
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#72SAMtools自带的统计命令–idxstats、stat、flagstat、bedcov和 ...
SAMtools 不仅仅用来call snp。从samtools的软件名就能看出，是对SAM格式文件进行操作的工作，比如讲sam转成bam格式，index，rmdup等等。samtools ...
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#73008-处理SAM、BAM你需要Samtools - Yunze Liu
008-处理SAM、BAM你需要Samtools · 1-based coordinate system ：序列的第一个碱基设为数字1，如SAM,VCF,GFF,wiggle格式 · 非常多的序列（read)，mapping到 ...
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#74cannot configure or make install samtools 0.1.19 - Ask Ubuntu
If you really want to compile samtools , then you do not need to run ./configure script (as it does not exist), just use make :
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#75Tutorial 1: Wrapping samtools sort
samtools : the command. · sort: the subcommand. Together, the command and subcommand form the base command. · -O bam the format of the output file. · -T tmp_: the ...
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#76Samtools常用命令的总结
samtools view [options] in.sam|in.bam|in.cram [region...] -f 提取## -f 4 提取出没有mapping上的reads -F 过滤## -F 4 过滤掉没有mapping上 ...
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#77"htsjdk.samtools.SAMFormatException: Invalid GZIP header ...
I am getting this error when I running VariantRecalibrator(my gatk version is 4.1.8.0): htsjdk.samtools.SAMFormatException: Invalid GZIP...
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#78Samtools on Rivanna - UVA Research Computing
Convert SAM to BAM with Samtools. samtools view can convert human-readable SAM files to binary BAM files. Below is a simple command to convert ...
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#79SAMtools-Teaching - Research Computing Center Wiki
Category. Bioinformatics. Program On. Teaching. Version. 0.1.20, 1.9, 1.10. Author / Distributor. SAMtools. Description.
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#80在Window7平台利用samtools尋找SNPs / INDELs - 有勁的基因 ...
在先前的部落格中我們介紹過了在Windows 7平台下利用bowtie或bowtie2將NGS定序的資料和reference序列作alignment，並利用samtools進行檔案的處理以及 ...
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#81samtools常用命令详解 - 陈连福的生信博客
view命令中，对sam文件头部的输入(-t或-T）和输出(-h)是单独的一些参数来控制的。 Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]] ...
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#82SAMtools - Wikiwand
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM , BAM and CRAM formats ...
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#83samtools Tutorial - Quinlan Lab
To convert SAM to BAM, we use the samtools view command. We must specify that our input is in SAM format (by default it expects BAM) using the - ...
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#84SAMtools - PACE Cluster Documentation
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM, and CRAM formats.
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#85SAMtools paper - GigaScience
How did Sequence Alignment/Map (SAM) format files and SAMtools come into being? This started when the 1000 Genomes Project wanted to move away ...
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#87SAMtools - ScientificComputing
Samtools is a set of utilities that manipulate alignments in the BAM format. It imports from and exports to the SAM (Sequence Alignment/Map) ...
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#88samtools 功能介绍_嘻皮悠 - 新浪博客
index 为sort后的bam文件建立所以，这是在view 比对结果时指定染色体区域必须做的。 samtools index aln.sorted.bam. rmdup ...
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#89Samtools - BITS wiki
Samtools is the standard library to work on SAM, BAM (and in the future CRAM) files. A Samtools Java wrapper is available under the name ...
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#90Faster sorting of BAM files: SAMtools vs sambamba - Basepair
x, with support for parallel processing for sorting. We compared the sorting speed of a 25Gb unsorted BAM file with SAMtools and sambamba. Our ...
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#91Ruby bindings for SAMtools, a library for accessing BAM files ...
The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM ...
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#92Samtools - Research Computing Documentation
Description. From the Samtools Home Page: Tools (written in C using htslib) for manipulating next-generation sequencing data ...
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#93Bioinformatics in Aquaculture: Principles and Methods
Alternatively, users can convert this to a BAM file and sort it by using other programs (e.g., SAMtools), or obtain “Aligned.out.bam" directly by setting ...
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#94Bioinformatics Data Skills: Reproducible and Robust Research ...
I won't cover the details of converting between binary, hexadecimal, and decimal number systems because the command samtools flags can translate bitflags ...
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#95Python for the Life Sciences: A Gentle Introduction to ...
A full step-by-step installation guide for samtools and bwa is beyond the scope of this chapter, but each of the tools has fairly complete installation ...
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#96Introduction to Bioinformatics with R: A Practical Guide for ...
Let's say that we want to use the Samtools set of programs for manipulating sequence data files. We first need to retrieve the file from the internet.
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