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bwa_mem_mapping

Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection

clone_mapping

Pipeline for generating SUNK pileups from clone sequence data

cn_plotting

conifer_pipeline

Scripts for processing data using conifer

empprior

Using empirical data to inform branch-length priors for Bayesian phylogenetics

genomestrip_snakemake

ipython_notebooks

lcadre

LCaDRE: Library Complexity and Duplication Rate Estimation

mrsfast

mrsFAST: micro-read substitution-only Fast Alignment Search Tool

mrssnake

Simple mrsfast read depth mapping using snakemake

pairsamtools

a legacy repo to avoid breaking existing pipelines

phylo-amp

Assessing model fit using posterior prediction

popfastaaa

Simple stand-alone programs for analysis of aligned Multi-FASTA formated files.

rd_custom_contig

Code for getting read depth-based copy number for a custom contig

read_depth_genotyper

Get genotypes for regions using WSSD and SUNK

segdup_phylogenetic_analysis

Pipeline based on phylogenetic methods in Sudmant et al. 2015 (SGDP)

sourmash

Quickly search, compare, and analyze genomic and metagenomic data sets.

ssf_dts_caller

scale space filtering based CNV calling and genotyping

stream_read_pair

vcflib

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

vh_pipeline

Variation Hunter pipeline using snakemake

vst_calc

Calculate Vst statistics for populations

wssd_sunk

Legacy codebase for WSSD and SUNK read depth file creation and analysis

xhmm_pipeline

Snakemake pipeline for running XHMM