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abc_inferences

admixtools

Tools test whether admixture occurred and more

admixturepipeline

A pipeline that accepts a VCF file to run through Admixture

ancestry_pipeline

Provides helper scripts for inferring local ancestry, performing ancestry-specific PCA, etc

angsd

Program for analysing NGS data.

anopheles_gambiae_structure_lvb

Scripts to analyze population structure of Anopheles gambiae mosquitoes in Lake Victoria basin.

assemble_pipeline

Assemble and following pipeline used in wisent genome paper.

atenuis_wgs_pub

Acropora tenuis paper

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bio_tools

Useful bioinformatic scripts

biomi609spring2022

This repository contains curricular material, lecture notes, labs, assignments, exams, code, solutions from the Spring 2022 version of BIOMI 609 Computational Genomics and Bioinformatics offered at San Diego State University.

biostack

camel_genomics

Code for the analysis of 25 Camel genomes

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi, using custom or published models for one to three populations.

deeplearning-biology

A list of deep learning implementations in biology

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

demographicinference

Scripts to compare models of divergence using diffusion approximation (dadi)

dsuite

Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species

easysfs

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

ejaghamcoptodon

Scripts used for the paper "Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids".

embopopgen2017

EMBO Practical Course: Population Genomics: background and tools

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

fine_structure

gelada-genome

gene_prediction

Gene prediction pipeline. FROM LZU.

genomics_general

General tools for genomic analyses.

grenepipe

Snakemake pipeline for variant calling from raw sequences

hellow-world

ic_selection

Code for model selection via five information criteria: Akaike's information criterion (AIC), the corrected AIC for finite length observations (AICc), Bayesian information criterion (BIC), two-stage Minimum Description Length (MDL) and normalized Minimum Description Length (nMDL). The dictionaries are the Frequency (Fourier) dictionary and the Frequency + Spike dictionary. Model selection is performed with Orthogonal Matching Pursuit or the simple Threshold method.

ils_simulation

ILS simulation process