Blog

Tricks make life easier

• Set up passwordless ssh login to remote server

Bioinformatics

Notes

• Dr. Eric C. Anderson's Bioinformatics Handbook

Variant calling related

• Prepare reference_genome.fasta

I. Single nucleotide variants and short insertions/deletions (SNVs and INDELs)

GATK

• GATK Data Pre-processing
• GATK Somatic Short Variant Discovery
• GATK Somatic copy number variant discovery (CNVs)
• Run GATK older version by docker images

From fastqs to bam

• Quality control for fastqs
• Align fastqs to reference genome

Filter bam

• Filter bam using samtools
• Filter bam using gatk

Other

• Different variant callers
• GEM: Reference genome mappability
• freebayes: Bayesian genetic variant detector
• SomaticSniper: SNVs and short Indel caller
• Strelka: SNVs and short Indel caller
• RTG Tools: compare vcf
• Control_FreeC: calculate tumor purity
• readtagger: tag reads using bams
• SomaticSeq: combine multiple SNV calls

II. Structural variants (SV)

Tools

• LUMPY: SV caller
• DELLY: SV caller
• svtools: comprehensive utilities for SV
• novoBreak: a structural variant breakpoint detection tool
• svParser: a tool to deal with SV output vcf
• Manta: SV caller
• GRIDSS2: SV caller
• SURVIVOR: merge SVs
• gGnome: post-visualization tool for SV

III. Copy number variation (CNV)

Tools

• CNVkit: CNV caller

Other data type

Long-read DNA

• pbsv: identify SV using long-read DNA
• deTEct: identify TE using long-read DNA

16s RNA

• 16sRNA: microbiome classification and abundance

Protein

• DiaNN

Transposable elements (TEs)

• dnaPipeTE

Toolbox

• SRA: Download data from NCBI
• Cypress: Tulane HPC
• sshfs: Mount a remote server

Programming

Linux

• Linux basics
• Basic shell scripting
• Activate conda in a bash script

Python

• Python scipy.integrate for numerical integration

Java

• IntellJ: Java IDEA

Format

• Enhanced styles

Tools

• Git clone from a private repository

Statistics

Theory

• Detailed Balance Condition
• Stochastic Processes
• Stochastic HW2 Graph
• Gibss sampler
• Kingman’s coalescent

Tools

• BEAST: Bayesian Evolutionary Analysis Sampling Trees
• RavBayes: Bayesian phylogenetic inference model

Research related papers

• Statistical phylogenetics study resources
• 2020Ji - Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics
• 2023Fourment - Automatic differentiation is no panacea for phylogenetic gradient computation

Learning interests

• Time Series
• Survival Analysis

Tulane footprint

• Tulane Courses