travc Goto Github PK

agam-aaeg-crispr-cas9-and-cas12a-target-sites

CRISPR-Cas9 and Cas12a Target Site Richness Reflects Genomic Diversity in natural populations of Anopheles gambiae and Aedes aegypti mosquitoes

analysis-examples

WGS analysis examples and skeletons

bcbio-nextgen

Validated, scalable, community developed variant calling and RNA-seq analysis

calling_aaegl5nuc

variant calling pipeline using snakemake

cas9_target_site_survey

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes from natural populations

chamber_control

Enviromental chamber monitoring and control

gambiae-dispersal

An. gambiae transcontinental dispersal analysis (2019)

gittemp

Misc temp stuff

gpat

A version Zev Kronenberg's vcflib tools

host_choice_gwas_arabiensis

ish_parser

Parser for NOAA ISH Files

locbatch

Acoustic Localization : Batch processing of wired-array data

mutation-rate

ngs_scripts

outbreak-reporter

Generate reports for Medfly outbreaks

paper-predicted-mf-quarantine-length

paper and supplemental materials for Evaluation of predicted medfly (Ceratitis capitata) quarantine length in the United States utilizing degree-day and agent-based models

paper-predicted-mf-quarantine-length-data-and-code

Data and code for the paper "Evaluation of predicted Medfly (Ceratitis capitata) quarantine length in the United States utilizing degree-day and agent-based models"

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

raddle

The Raddle software for Rare-Allele-based Distance of Dispersal Estimation, based on Novembre & Slatkin (2009)

sambamba

Tools for working with SAM/BAM data

slides

slides, talks, and stuff like that

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

vcfnp

Load numpy arrays and HDF5 files from VCF (variant call format)

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

vt

A tool set for short variant discovery in genetic sequence data.

yam

Repository containing scripts and datasets used for the study of African Yam (Dioscorea rotundata) domestication history