一、NCBI各类数据储存库
1、Sequence Read Archive (SRA)：raw sequence data and alignment information from
high throughput sequencing platforms including 454, illumina, SOLiD and PacBio.
2、Gene Expression Omnibus (GEO)：RNA-Seq, ChIP-seq, RIP-seq, HiC-seq, methyl-seq, expression data such as microarray, SAGE or mass spectrometry data sets.
3、Database of Short Genetic Variations (dbSNP)：variation data, such as single nucleotide variations, microsatellites, and small-scale insertions and deletions.
4、Database of Genomic Structural Variations (dbVar)：genomic structural variation data, such as large insertions, deletions, translocations etc.
5、Database of Expressed Sequence Tags (dbEST)
6、Transcriptome Shotgun Assembly Sequence Database (TSA)：transcriptome assemblies
7、Whole Genome Shotgun Submissions (WGS)：incomplete genome assemblies.
二、Entrez
如何使用Entrez？NCBI提供了一个API网络接口Entrez E-utilsand 和一个命令行工具Entrez Direct。
Entrez E-utils
query URL ：https://service.nih.gov?param1=value1¶m2=value2
在shell中，&需要使用转义符\，或者将URL添加引号‘’
curl -s https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? id=AF086833.2\&db=nuccore\&rettype=fasta|head
curl -s 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?id=AF086833.2&db=nuccore&rettype=fasta'|head
具体命令参考文档：https://www.ncbi.nlm.nih.gov/books/NBK25500/
Entrez Direct
具体命令参考文档：https://www.ncbi.nlm.nih.gov/books/NBK179288/
einfo
抓取描述信息，einfo -dbs 查看所有数据库类型
esearch
esearch -help 查看帮助，esearch 查找的记录可以传递给efetch下载
esearch -db .. -query .. | efetch -formate ..
esearch -db sra -query PRJNA257197 | efetch -format runinfo > info.csv (runinfo — 所有搜索的信息)
efetch
It can even produce the sequence from reverse strands(reverse complement):
三、sratoolkit
1、prefetch 可以从远程站点下载文件
prefetch --option-file ids.list
2、fast-dump : downloads data in FASTQ format, 初始sra data 保存在 ~/ncbi/public/sra/
fastq-dump SRR1553607 --split-files( separate paired end reads)
下载project里多个SRA数据：
在上一步得到的info.csv文件中，第一列为这个project里所有的SRA文件，取第一列run编号，用xargs批量下载
cat info.csv|cut-f 1 -d','|grepSRR|head>ids ； cat ids |xargs-n 1 fastq-dump -X 10000 --split-files $1
3、sra-stat
sra-stat --xml --quick SRR1553610 生成xml报告
四、 SeqKit
seqkit stat *.gz 查看全部fasta/q文件的简要信息
seqkit fx2tab --name --only-id --gc *.fna 显示GC含量
seqkit fx2tab -H -n -i -B a -B c -B ac *.fna 显示A、C、AC含量
随机取出0.001比例的id号，并根据id从总体中提取序列：seqkit sample --proportion 0.001 duplicated-reads.fq.gz|seqkitseq --name --only-id>id.txt ；seqkit grep --pattern-file id.txt duplicated-reads.fq.gz > duplicated-reads.subset.fq.gz
seqkit grep --pattern-file id2.txt --invert-match viral.1.1.genomic.fna.gz > clean.fa 取出list上的序列
seqkit grep --pattern-file id2.txt viral.1.1.genomic.fna.gz|seqkitlocate--ignore-case --only-positive-strand --pattern K+ --pattern N+ 显示含K、N的数据
seqkit rmdup --by-seq --ignore-case duplicated-reads.fq.gz 去除重复
seqkit locate --degenerate --ignore-case --pattern-file enzymes.fa *.fna 匹配短序列如酶结合位点
seqkit sort--by-length／full header (--by-name) or sequence content (--by-seq)
seqkit split --by-id --id-regexp"\[(.+)\]" 根据ID, number of parts, size of each part, or sequence region分离
csvtk join-H -t<(seqkit fx2tab 1.fa)<(seqkit fx2tab 2.fa)|sed's/\t\t//'|seqkit tab2fx 合并两个文件
五、other tool
get subreads from a single ZMW : bamtools filter -in subreads.bam -out zmw.bam -tag 'zm..'
get the consensus sequence from the subreads : # ccs [options] INPUT OUTPUT