Pinned Repositories
AMEB2020_Phylogenomics_demo
docker-intro
A short introduction to using Docker in Bioinformatics
genomisc
The repository contains a set of miscellaneous scripts for working with various kinds of genomics data.
maker-docker
Docker image as base for building full MAKER image
maker2gff_to_sqn
methylkit-docker
MITObim
MITObim - mitochondrial baiting and iterative mapping
MitoFish2tbl
Convert MitoAnnotator (MitoFish) annotation file to NCBI feature table format (*.tbl)
phylogenomics_intro_vertebrata
Phylogenomics tutorial based on BUSCO genes
short-read-processing-and-assembly
A short introduction to processing and assembly of short (Illumina) NGS sequencing data
chrishah's Repositories
chrishah/kmc3-docker
Docker image for kmc3
chrishah/CONCOCT
Clustering cONtigs with COverage and ComposiTion
chrishah/mono_prelim
chrishah/leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
chrishah/fasconcat-g
Ubuntu 16.04 with FASTconCAT v1.04 installed
chrishah/raxml-docker
Ubuntu 18.04 with RAxML 8.2.12 installed.
chrishah/alicut-aliscore-docker
Ubuntu 16.04 with ALISCORE v2.0 and AliCUT v2.31
chrishah/clustalo-docker
Ubuntu 16.04 with clustalo 1.2.4 installed
chrishah/ectools-docker
Docker image containing a full install of ectools
chrishah/premaker-plus-docker
Docker image as base for building full MAKER image
chrishah/hicup-docker
Docker image containing a full HiCUP install
chrishah/ONT-stuff-docker
chrishah/pyScaf-docker
Docker image containing a full PyScaf install
chrishah/pyScaf
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
chrishah/maker2gff_to_sqn
chrishah/Porechop
adapter trimmer for Oxford Nanopore reads
chrishah/aMITO_MiMB
chrishah/tutorials
Tutorials on evolutionary genomics
chrishah/SNPGenie
Perl software for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
chrishah/PIrANHA
Scripts for file processing and analysis in phylogenetics and phylogeography
chrishah/desatetrth-mt
chrishah/turn
chrishah/mptp
mPTP - a tool for single-locus species delimitation
chrishah/nextflow-annotate
Workflows I find helpful for fungal genome annotation
chrishah/gyrosim
chrishah/mb_notebook
chrishah/python-basic
Docker image with essentials for basic python scripting
chrishah/GSA_tutorial
Gene-set analysis tutorial
chrishah/gyrophil
chrishah/SNAP
Gene prediction software