FASTQ format 每个FASTQ文件中每个序列通常有四行信息: 1: 以 '@' 字符开头,后面紧接着的是序列标识符和可选字段的描述(类似FASTA title line). 2: 序列 3: 以 '+' 字符开头, 后面紧接着的是可选字段的描述性信息 4: 第二行序列的质量信息 Illumina sequence identifiers @HWUSI-EAS100R:6:73:941:1973#0/1 sequence identifiers description HWUSI-EAS…

http://wiki.bits.vib.be/index.php/Identify_the_Phred_scale_of_quality_scores_used_in_fastQ # S - Sanger Phred+33, raw reads typically (0, 40) # X - Solexa Solexa+64, raw reads typically (-5, 40) # I - Illumina 1.3+ Phred+64, raw reads typically (0, 4…

http://www.molecularevolution.org/resources/activities/QC_of_NGS_data_activity_new table of contents expected learning outcomes getting started exercise 1: checking Illumina data with the FASTX-Toolkit exercise 2: checking 454 data with the FASTX-Too…

链接:Canu Tutorial Canu assembles reads from PacBio RS II or Oxford Nanopore MinION instruments into uniquely-assemblable contigs, unitigs. Canu owes lots of it design and code to celera-assembler. Canu can be run using hardware of nearly any shape or…

http://sourceforge.net/projects/het-smooth/ equencing technologies, such as Illumina sequencing, provide the sequences ofshort "reads" of DNA that come from random positions on the genome. These readsthen must be assembled de-novo into the origi…

改编: python ~/tools2assemble/run_fastuniq.py SHT-3K-1_1.fq.gz SHT-3K-1_2.fq.gz 好像不支持gz文件,要先解压 http://sourceforge.net/projects/fastuniq/ 下载: http://sourceforge.net/projects/fastuniq/files/FastUniq-1.1.tar.gz/download 如果下载下来文件名是download 改一下名字 这是个tar.gz文…

https://www.biostars.org/p/198405/ Quick question is: I have some mapped reads in bam file which have good read quality, but they have sam flag 0x200 which means they didn't pass the vendor check. Should I include them or not in downstream analysis?…

本文近期更新地址: http://blog.csdn.net/tanzuozhev/article/details/51077222 随着測序技术的不断提高.二代測序数据成指数增长. NCBI提供了SRA数据库存储这些数据. http://www.ncbi.nlm.nih.gov/sra 为了方便更好的分析这些数据,NCBI提供了下载的命令行工具:sra-toolkit. 包含下面命令: 官方文档: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi…

测序数据中经常会接触到fastq格式的文件,比如说拿到fastq格式的原始数据后希望查看测序碱基的质量并去除低质量碱基.一般而言大家都是用现有的工具,比如说fastqc这个Java写的小程序,确实很好用,运行速度快,检查的项目也多.有时候我们也需要对这些数据进行个性化的分析,那么这个时候这些小工具就不能胜任了,需要我们自己写程序(脚本)来处理.本人目前才疏学浅,因此只有一下三种方案: 1.完全自己写脚本,读取每一行,手动解析,然后实现个性化分析.(显然这个比较慢,相当于重造了一个转速很慢的轮子)…

1)知识简介--------------------------------------------------------1.1)测序质量值 首先在了解fastq,fasta之前,了解一下什么是质量值.phred软件在对reads进行base calling的时候会给出每一个碱基的质量值,这个质量值的计算与测序预期错误率相关(estimated probability of error): Phred Quality Score     Probability of incorrect bas…