thedbstern Goto Github PK

baltic_lab_wild

Scripts and data associated with "Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod"

cbi_reference_databases

Tools for building reference databases

consiter

Python script to generate a reference-guided viral consensus sequence using an iterative mapping and variant calling approach

crustacean_hic

Pipeline for aligning and processing Crustacean HiC data

filter_reads

Scripts to filter sequence reads of microbial contamination

hpv-genotyping

Collection of scripts and commands for analyzing Illumina-sequence-based HPV genotyping data

interspecific_rnaseq

minima

Minima is a one-size-fits-all Jekyll theme for writers.

nee2020

Scripts to facilitate the analyses (post SNP-calling) of Stern and Lee 2020. Evolutionary origins of genomic adaptations in an invasive copepod

phylode

poolseq_utils

Scripts to process allele frequency files used in PoolSeq analyses

recombination_simulations_phylo

researchanalyticslabs

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

rnaseqqc_alignment

Introductory practical training

sicb2018

thedbstern.github.io

David B. Stern website

toga

viral-assembly-variant-calling

Snakemake pipeline to assemble a viral consensus sequence, and optionally call SNPs and haplotypes