lottpaul/DoesNaughtCompute

Code and example datasets for Does[0]Compute

Does[0]Compute Fall 2016 – Spring 2017 Syllabus

Topics Covered

• File Conversions and Other Utilities
• Sequence Cleaning and Quality Control
• Read Mapping with Short and Long Read Aligners
• SAM Processing
• Genomic Ranges
• Variant Detection
• Variant Annotation
• Quantitiave Genetics
• Population Genetics

Tentative Dates

We meet every Tuesday from 2:00 PM to 3:00 PM in 213 Boralug Hall for the Spring 2017 semester

January 24^th, 2016: sequence_handling

Discussion Leader: Fernanda Rodriguez

January 31^st: CANCELED

February 7^st: Variant Detection

Discussion Leader: Li Lei

• GATK Part I
  • Paper

February 14^th: Variant Detection

Discussion Leader: Peter Morrell

• Freebayes
  • Paper
• SAMTools mpileup/bcftools
  • SAMTools SNP Calling Paper
  • bcftools Paper
  • SAMTools Mapping to Variant Calls

February 21^st: Variant Detection

Discussion Leader: Paul Hoffman

• VCFtools
  • Paper
• Platypus
  • Paper
• Summary Paper

February 28^th: Variant Annotation

Discussion Leader: Tom Kono

• BAD_Mutations
• ANNOVAR
  • Paper

March 7^th: Quantitiave Genetics

Discussion Leader: Li Lei

• R/QTL Part I
  • Paper

March 14^th: Quantitiave Genetics

Discussion Leader: Tom Kono

• R/QTL Part II
  • Paper

March 21^st: Quantitiave Genetics

Discussion Leader: Alex Olhoff

• R NAM

March 28^th: Big Data Visualization

Discussion Leader: Alex Olhoff

April 4^th: Quantitiave Genetics

Discussion Leader: Peter Morrell

• BEAGLE
  • Phasing Paper
  • Imputing Paper
  • IBD Detection Paper
• PHASE/fastPHASE
  • PHASE Paper
  • fastPHASE Paper

April 11^th: Population Genetics

Discussion Leader: Chaochih Liu

• ANGSD/ANGSD-wrapper Part I
  • ANGSD Paper
  • ANGSD-wrapper Paper

April 18^th: Population Genetics

Discussion Leader: Chaochih Liu

• ANGSD/ANGSD-wrapper Part II
  • ANGSD Paper
  • ANGSD-wrapper Paper

April 25^th: Population Genetics

Discussion Leader:

• hierfstat
  • Paper
• LDhat

May 2^nd: 10xgenomics data analysis

Discussion Leader:John R Garbe in UMGC

• Pending

May 9^nd: Population Genetics

Discussion Leader:

• STRUCTURE
  • Paper
• ADMIXTURE
  • Paper

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Fall 2016 Meetings and Materials

September 22^nd, 2016: File Conversions and Other Utilities

Discussion Leader: Li Lei and Paul Hoffman

• UNIX sort
• Plink 1.9 Part I
  • Paper

September 29^th, 2016: File Conversions and Other Utilities

Discussion Leader: Chaochih Liu

• Plink 1.9 Part II
  • Paper

October 6^th, 2016: Sequence Cleaning and Quality Control

Discussion Leader: Paul Hoffman

• FastQC
• FASTX-toolkit

October 13^th, 2016: Sequence Cleaning and Quality Control

Discussion Leader: Chaochih Liu

• Seqqs
• Sickle
• Scythe

October 20^th, 2016: Short Read Aligners

Discussion Leader: Peter Morrell

• Recommended Reading
  • Clegg and Morrell, 2004, Bioinformatics
  • Clegg and Morrell, 2004, Mutational Processes
• BWA
• Bowtie 2
  • Paper

October 27^th, 2016: Short Read Aligners

Discussion Leader: Ying Zhang

• Benchmarking short sequence mapping tools
• BWA
• Bowtie 2
  • Paper

Novermber 3^rd, 2016: Long Read Aligners

Discussion Leader: Kevin Silverstein and Corey Carter

• BLASR
• MHAP
• DALINGER
  • Comparison Paper

November 10^th, 2016: SAM Processing

Discussion Leader: Li Lei

• SAMTools
  • Paper
• Picard

November 17^th, 2016: SAM Processing

Discussion Leader: Colin Pierce

• SAMTools
  • Paper
• Picard

December 1^st, 2016: Advanced Software Installation

Discussion Leader: Paul Hoffman

• GCC/G++
• configure
• GNU Make
• CMake
• Java programs
• setup.py
• Modulefiles

December 8^th, 2016: CANCELED

December 15^th, 2016: Genomic Ranges

Discussion Leader: Chaochih Liu

• BEDTools
  • Paper
• BEDOPS
  • Paper