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2023-01-31-genomicsdc

bioawk-tutorial

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

carpentries-workshop

corvid_svpopgen

course20

Deep Learning for Coders, 2020, the website

deeplearning-biology

A list of deep learning implementations in biology

drosophila_indels

Barton and Zeng (2018) - Pipeline and scripts for popgen analysis of whole-genome drosophila data.

dsim_variant_pipeline_ref_v2.02

edta

Extensive de-novo TE Annotator

ehux_hd

feelnc

FEELnc : FlExible Extraction of LncRNA

genome_annotation

These are scripts that I use frequently in genome annotation projects. Some of them have evolved awkwardly so the code is difficult to follw

genome_scripts

collection of random scripts for processing genome related files. the shell scripts are specific to my environment and may not work elsewhere.

genometricorr

Testing out the GenometriCorr R package

javibio-git.github.io

kat

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

matsumoto_akashi_aipoly_codes

merqury

k-mer based assembly evaluation

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mutation_unphased

np_tut_breastcancer

Numpy and matplotlib tutorial for beginners using a breastcancer dataset

orthnet

CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology

parsing-repeatmasker-outputs

Few scripts facilitating the extraction of info from Repeat Masker .out files

pbipa

Improved Phased Assembler

pegoscapus_annotation_project

This repository details the protocol used to conduct a comprehensive genome annotation using Maker.

pilon

Pilon is an automated genome assembly improvement and variant detection tool

repenrich2

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

rescan

A command line tool for inferring the locations of repeat expansions and other structural variation from paired-end short read sequencing data

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.