kongdeju / ngstools

Next-Generation Sequencing(NGS) toolkits.

NGSTools : Next-Generation sequencing toolkits

Author: Czh3 [email protected]

High-throughput sequencing technology is repaidly becoming the standard method for genomics, transcriptomic and epigenetics. The down stream data analysis is sophisticated because of the unprecedented data throughput. This NGSTools helps you to do this easily by writing a few lines of script.

###For illumina sequencing platform:

• Hiseq 2000
• Hiseq 2500
• HiseqX-Ten/Five
• Hiseq 3000
• Hiseq 4000
• Miseq

###Based on:

• python::Bio
• fastqc
• fastx
• cutadapt
• SAMtools
• picard
• GATK
• HTseq
• cufflinks
• DEseq2

This package help you to build your own pipeline easily.

Examples pipeline:

Here are several examples of NGS pipelines.

###mRNA sequencing

python2.7 ~/bin/NGSTools/RNA_pipeline.py --sampleList sample.list\
	-d raw  -o pipe_out -c ~/.mouse.cfg\
	-a 1,2

python RNA_pipeline.py -h
usage: RNA_pipeline.py [-h] -s SAMPLELIST [-o OUTDIR] [-d {raw,clean}]
                       [-a ANALYSIS] [-c CONFIG] [--debug DEBUG]

A pipeline of RNA_seq data analysis. <[email protected]>

optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLELIST, --sampleList SAMPLELIST
                        sample list for RNA samples information.
                         A file each line contains:
                        sampleName	sampleCondition	fastq1Path	fastq2Path
  -o OUTDIR, --outDir OUTDIR
                        The pipeline output dir
  -d {raw,clean}, --dataType {raw,clean}
                        fastq data type:
                        raw data or clean data.
                         if (clean data): not run cutadapter
  -a ANALYSIS, --analysis ANALYSIS
                        analysis of the pipeline to do.
                        Here is some software to choose to analy
                        [1:QC, quality control
                         2:Mapping, align the reads to reference genome
                         3:Cufflinks, assemble with cufflinkes 
						 4:DESeq2, call DEGs(different expression genes) using DESeq2 package
                         5:DEXSeq, call DEUs(different exon usages) using DEXSeq package
                         6:GATK, call SNP on mRNA using GATK]
  -c CONFIG, --config CONFIG
                        the config file of NGSTools package.
  --debug DEBUG         debug mode

###BS sequence pipeline (WGBS,RRBS)

python ~/bin/NGSTools/BS_seq.py -s sample.list 	\
	-o result 	\
	-c /home/zhangc/.mouse.cfg 	\
	-r -a 1,2,7

python ~/bin/NGSTools/BS_seq.py -h
usage: BS_seq.py [-h] -s SAMPLELIST [-o OUTDIR] [-c CONFIG] [-r] [-a ANALYSIS]
                 [--debug DEBUG]

A pipeline of Bisulfite-Seq(WGBS and RRBS) data analysis. <[email protected]>

optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLELIST, --sampleList SAMPLELIST
                        sample list for RNA samples information.
                         A file each line contains:
                        sampleID	sampleName	fastq1Path	fastq2Path
  -o OUTDIR, --outDir OUTDIR
                        The pipeline output dir
  -c CONFIG, --config CONFIG
                        the config file of NGSTools package.
  -r, --rrbs            for RRBS library
  -a ANALYSIS, --analysis ANALYSIS
                        analysis of the pipeline to do.
                        Here is some software to choose to analy
                        [1:QC, quality control
                         2:bismark, align the reads to reference genome
                         3:bs_seeker2, align the reads to reference genome
                         4:picard_rmdup, remove PCR duplicates using picard
                         5:BS_SEEK2_methylation_extractor, call methylation levels using the tools in bismark
                         6:swDMR, call methylation levels using swDMR]
                         7:bismark_methylation_extractor
  --debug DEBUG         debug mode

WGS pipeline

python WGS.py --help
usage: WGS.py [-h] -s SAMPLELIST [-o OUTDIR] [-c CONFIG] [-a ANALYSIS]
              [-b QBASE] [--debug DEBUG]

A pipeline for WGS data analysis. <[email protected]>

optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLELIST, --sampleList SAMPLELIST
                        sample list for RNA samples information.
                         A file each line contains:
                        sampleID	sampleName	fastq1Path	fastq2Path
  -o OUTDIR, --outDir OUTDIR
                        The pipeline output dir
  -c CONFIG, --config CONFIG
                        the config file of NGSTools package.
  -a ANALYSIS, --analysis ANALYSIS
                        analysis of the pipeline to do.
                        Here is some software to choose to analy
                        [1:QC, quality control
                         2:Mapping, align the reads to reference genome
                         3:picard_rmdup, remove PCR duplicates using picard
                         4:mpileup, call SNP using samtools mpileup]
  -b QBASE, --qbase QBASE
                        quality base of base calling: 33(default) or 64
  --debug DEBUG         debug mode

###MeDIP pipeline

python ~/bin/NGSTools/MeDIP.py -s sample.list	\
	-o result	\
	-c ~/.mouse.cfg

python ~/bin/NGSTools/MeDIP.py -h
usage: MeDIP.py [-h] -s SAMPLELIST [-o OUTDIR] [-c CONFIG] [-a ANALYSIS]
                [--debug DEBUG]

A pipeline for MeDIP data analysis. <[email protected]>

optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLELIST, --sampleList SAMPLELIST
                        sample list for RNA samples information.
                         A file each line contains:
                        sampleID	sampleName	fastq1Path	fastq2Path
  -o OUTDIR, --outDir OUTDIR
                        The pipeline output dir
  -c CONFIG, --config CONFIG
                        the config file of NGSTools package.
  -a ANALYSIS, --analysis ANALYSIS
                        analysis of the pipeline to do.
                        Here is some software to choose to analy
                        [1:QC, quality control
                         2:BWA, align the reads to reference genome
                         3:Filter Bam, get properly matched reads 4:picard_rmdup, remove PCR duplicates using picard
  --debug DEBUG         debug mode