Giter VIP home page Giter VIP logo

insilicoradseq's Introduction

inSilicoRADSeq

Repository of the Masters thesis project in computational biology titled: "In silico RAD-Seq as a possible tool for ancestry determination: an application in Helicobacter pylori"

  1. Simulation reads of the reference genome: simread_WholeGenome_wgsim.sh
  2. Restriction enzymes fragment generations for RAD-Seq and ddRAD-Seq simulations: ddRADseqTools_Hpylori_Frags.sh
  3. Form the Fragments .fasta files in step 2 to generate illumina simulations of Pared End (PE_ReadSim.sh) and Single End (SE_ReadSim.sh). To run this illumina simulations the script needs the java project SimpleReadsSim.zip.
  4. From the illumina .fastq files in step 3 reads are mapped to the reference genome of the PE and SE reads: runBWA_PE.sh and runBWA_SE.sh
  5. Finding SNPS form the .bam files in step 4. :MultipleVariantCall_NGSEP.sh To run correctly this script need the .bai files form step 4, even though they are not used explicity called in the script.
  6. Build distance matrix from the .vcf files in step 5 and calculate the Neighbor joining dendrograms: MatrixDistance-NJ.sh
  7. Run structure analysis with StrAuto pipeline (http://strauto.popgen.org) from STR file: runStrAuto.sh To run this file convert the vcf file in step 5 to str with software PGDSpider_2.1.1.5 (http://www.cmpg.unibe.ch/software/PGDSpider/)
  8. Plot structure analysis: structurePlot.m. To run this file use only the probability of each population (columns) of each sample (rows) once the best k has been chosen.

insilicoradseq's People

Contributors

cpulloa avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.