rm-seq是一种生物信息学工具，用于评估pe短读的抗性突变。
rmseq的Python项目详细描述
用于高通量评估的生物信息管道分析 抗药性突变。RM seq是一种基于扩增子的深度测序 单分子条码技术。我们采用了这种方法 鉴定和鉴定抗生素耐药突变。
提供了RM seq工作流的完整描述 here
这是适合我的工具吗？
- 为了能让我们看到这条管道，你需要有序列放大器 分子条码库。
- 它只支持成对的结束fastq读取（包括压缩的.gz FastQ文件）。
- 它需要重叠的成对读取。
- 它需要测序基因（DNA）的参考Fasta序列 顺序）。
- 它是用Python3和Perl编写的
安装
安装RM seq管道
pip3 install rmseq
依赖性
RM seq具有以下包依赖关系：*EMBOSS>；=6.6 clustalo，cons，getorf，diffseq*欧米茄俱乐部= 1.2.1*bwa>；=0.7.15*samtools>；=1.3*bedtools>；=2.26.0*梨 >；=0.9.10*cd hit>；=4.7*trimmomatic>；=0.36*seqtk>；=1.3-r106 （仅当子示例读取时）*python模块：plumbum， Biopython
brew tap homebrew/science brew tap tseemann/bioinformatics-linux brew install parallel; parallel --citation # please write will cite brew install bedtools brew install EMBOSS brew install clustal-omega brew install bwa brew install samtools brew install pear brew install cd-hit brew install trimmomatic brew install seqtk pip3 install plumbum pip3 install biopython
快速启动
做
rmseq
帮助
usage: rmseq [-h] ...
Run RM-seq pipeline.
optional arguments:
-h, --help show this help message and exit
Commands:
run Run the pipeline.
version Print version.
check Check pipeline dependencies
test Run the test data set.
检查是否安装了依赖项
rmseq check
运行测试数据集
rmseq test
要运行分析管道，请执行
中的步骤rmseq run -h
usage: rmseq run [options]
Run the pipeline
positional arguments:
R1 Path to read pair 1
R2 Path to read pair 2
refnuc Reference sequence that will be used for premapping
filtering and mutation annotation (fasta).
outdir Output directory.
optional arguments:
-h, --help show this help message and exit
-d, --debug_on Switch on debug mode.
-f, --force Force overwite of existing.
-b BARLEN, --barlen BARLEN
Length of barcode (default 16)
-m MINFREQ, --minfreq MINFREQ
Minimum barcode frequency to keep (default 5)
-q BASEQUAL, --basequal BASEQUAL
Minimum base quality threshold used for trimming the
end of reads (trimmomatic TRAILING argument) (default
30)
-c CPUS, --cpus CPUS Number of CPUs to use (default 72)
-t TRANSLATION, --translation TRANSLATION
Manually set the reading frame for translation (use 1,
2 or 3 - use getorf by default)
-r MINSIZE, --minsize MINSIZE
Minimum ORF size in bp used when annotating variants
(default 200)
-w WSIZE, --wsize WSIZE
Word-size option to pass to diffseq for comparison
with reference sequence (default 5)
-s SUBSAMPLE, --subsample SUBSAMPLE
Only examine this many reads.
-k, --keepfiles Keep the intermediate files (default remove)
-n, --noaln Skip reads alignment when generating consensus (to use
for indel quantification only) (default align)
检查版本
rmseq version
输出
rm seq生成一个名为amplicons.effect的抽头分离输出文件 其中每一个raw对应一个一致的扩增子（在 按顺序排列的总体）：
| Column | Example | Description |
|---|---|---|
| barcode | GACACAACTGAGATTA | sequence of the barcode |
| sample | Rifampicin1 | output folder name |
| prot_mutation | H481N | annotation of the amino acid change (Histidine residue 481 substituted by Asparagine) |
| prot_start | 481 | start coordinate of the mutation |
| prot_end | 481 | end coordinate of the mutation |
| nuc_mutation | C1443G | annotation of the nucleotide change |
| nuc_start | 1443 | start coordinate of the nucleotide change |
| nuc_end | 1443 | end coordinate of the nucleotide change |
| prot | VRPPDKNNRFVGLYCTLV… | protein sequence of the consensus sequence |
| dna | GGTTAGACCACCCGATAA… | dna sequence of the consensus sequence |
| reference_barcode | CTGACACGTCCTGAAG | barcode of the identical consesnsus amplicon used for annotation |
RM seq生成的其他文件包括：
| File name | Description |
|---|---|
| amplicons.barcodes | Table with the count of each barcode sequence |
| amplicons.fna | Multifasta file containing all the consensus nucleotide sequence (header of sequence is the barcode) |
| amplicons.faa | Multifasta file containing all the consensus protein sequence (header of sequence is the barcode) |
| amplicons.fna.cdhit | Multifasta file containing all the unique consensus nucleotide sequence (header of sequence is the barcode) |
| amplicons.faa.cdhit | Multifasta file containing all the unique consensus amino acid sequence (header of sequence is the barcode) |
问题
请向Issues Page报告问题。
引文
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