chrishah/phylog

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Language
Perl
Created over 10 years ago
Updated over 8 years ago

chrishah/phylog

chrishah

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useful scripts for the preparation of phylogenomic data

MITObim

MITObim - mitochondrial baiting and iterative mapping

maker-docker

Docker image as base for building full MAKER image

maker2gff_to_sqn

MitoFish2tbl

Convert MitoAnnotator (MitoFish) annotation file to NCBI feature table format (*.tbl)

short-read-processing-and-assembly

A short introduction to processing and assembly of short (Illumina) NGS sequencing data

phylogenomics_intro_vertebrata

Phylogenomics tutorial based on BUSCO genes

methylkit-docker

post-assembly-intro

AMEB2020_Phylogenomics_demo

genomisc

The repository contains a set of miscellaneous scripts for working with various kinds of genomics data.

docker-intro

A short introduction to using Docker in Bioinformatics

phylogenomics-intro

Phylogenomics tutorial based on BUSCO genes

AMEB_2020_practical

demogenas

democratizing genome assembly

guppy-docker

Ubuntu 20.04 with ONT's Guppy basecaller

testing_CWL

prepro

Snakemake pipeline for intitial processing (trimming, errorcorrection, merging) of Illumina data

snakemaker

Snakemake pipeline to run genome annotation with MAKER

BUSCO-docker

Docker image containing a full BUSCO install

longstitch-docker

Debian 10 with longstitch scaffolding pipeline

cegma-docker

Docker image to run CEGMA in Ubuntu 14.04

Bioinformatics_cheat_sheets

Recipies for running some common bioinformatics software tools and workflows

porechop-docker

Ubuntu 18.04 with porechop installed