bergeycm

stuff-i-forget

Stuff I Routinely Forget How to Do

xspecies-exome

Analysis pipeline for cross species exome next-generation sequencing data

NGS-map

A general pipeline for mapping next-gen sequencing reads and calling variants

Anopheles_gambiae_structure_LVB

Scripts to analyze population structure of Anopheles gambiae mosquitoes in Lake Victoria basin.

DIY_bioinformatics_links

Links and resources for getting started with bioinformatics

rhg-convergence-analysis

Code used for "Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers"

RNAseq_workshop_2017

Code for RNAseq workshop run in July 2017

RAD-faex

Code used in the development of the "fecalseq" method for enriching host DNA from feces

vcf-tab-to-fasta

ABCtoolbox_power_analysis

awash-dopamine

Code used for analyses in Bergey et al 2016, "Dopamine pathway is highly diverged in primate species that differ markedly in social behavior"

BaitSTR

Automate the discovery of exact short tandem repeats (and its flanking region) from Illumina fastq sequences.

bedtools

A powerful toolset for genome arithmetic.

bergey-bioinfo

Home for random bioinformatic scripts.

codons-from-refgene

Given the refGene.txt database file (in ANNOVAR format), this R script outputs a BED file of the 1st, 2nd, or 3rd codons.

field-workers

fieldwork-packing-list

A list of things to bring when undertaking biological fieldwork

Kraken_db_install_scripts

Updated Kraken DB install scripts to cope with new-ish NCBI structure

tapeworm-genome-transcriptome-analyses

Code used in the analysis of tapeworm genomes.