sunbymoon / ngsclean-1 Goto Github PK
View Code? Open in Web Editor NEWThis project forked from mfumagalli/ngsclean-1
Pipeline for NGS read (filtering, trimming, merging) and SNP (quality, depth, biases, ...) quality control
This project forked from mfumagalli/ngsclean-1
Pipeline for NGS read (filtering, trimming, merging) and SNP (quality, depth, biases, ...) quality control
Pipeline for NGS data analysis ============================== The idea behind this script is have a simple way to go from raw FASTQ reads to BAM files. Briefly: 1) Read QC. % ./filter_reads.sh file_1.fastq file_2.fastq If file_2.fastq ommited assumes single end reads. 2) Read mapping. Not included here! Use your favorite read mapping program (eg. BWA, Bowtie2, SNAP, ...) 3) SNP QC % ./filter_SNP.sh run_ID $N_IND $CHR bam_list.txt $REF_SEQ $ANC_SEQ The output from this step is a BED file with the positions that passed the quality filters. This file can be used on all downstream analysis 4) Check VCF and SFS to assess overall quality of data. % Rscript analyze_vcf.R myvariants.vcf output_file Script Description ================== filter_reads.sh Script to perform raw reads QC. Namely, read filtering, quality trimming, adaptor trimming, PE read merging,... filter_SNP.sh SNP QC based on min/max depth, HWE, quality bias, strand bias, ... It calls the scripts below. get_mut_bias.pl Script to plot the mutation frequency bias along the read. It was developed to deal with ancient DNA. get_depth_thresh.R R script to automatically define the upper and lower depth coverage limits on SNPcleaner. It fits a mixture of Gamma and Neg-Binomial distribution to the empirical read coverage distribution. SNPcleaner.pl Filters sites from VCF files following a set of rules. analyze_vcf.R Script to visualize aspects of data in VCF files.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.