marcguery

AGAT

Another Gtf/Gff Analysis Toolkit

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

world_countries

Constantly updated lists of world countries and their associated alpha-2, alpha-3 and numeric country codes as defined by the ISO 3166 standard, available in CSV, JSON , PHP, SQL and XML formats, in multiple languages and with national flags included; also available are the ISO 3166-2 codes of provinces/ states associated with the countries

TRF

Tandem Repeats Finder: a program to analyze DNA sequences

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

bazam

A read extraction and realignment tool for next generation sequencing data

ggpattern

ggplot geoms with pattern fills

paper

Typora theme for the academy

tsv-utils

eBay's TSV Utilities: Command line tools for large, tabular data files. Filtering, statistics, sampling, joins and more.

DEploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

DEploid-r

An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

GECKO

THEREALMcCOIL

A Markov chain Monte Carlo method that estimates complexity of infection and population allele frequencies using SNP data obtained from Sequenom or similar types of SNP assays.