Pinned Repositories
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
read_depth_genotyper
Get genotypes for regions using WSSD and SUNK
bnelsj's Repositories
bnelsj/read_depth_genotyper
Get genotypes for regions using WSSD and SUNK
bnelsj/bwa_mem_mapping
Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection
bnelsj/clone_mapping
Pipeline for generating SUNK pileups from clone sequence data
bnelsj/cn_plotting
bnelsj/conifer_pipeline
Scripts for processing data using conifer
bnelsj/EmpPrior
Using empirical data to inform branch-length priors for Bayesian phylogenetics
bnelsj/genomestrip_snakemake
bnelsj/ipython_notebooks
bnelsj/lcadre
LCaDRE: Library Complexity and Duplication Rate Estimation
bnelsj/mrsfast
mrsFAST: micro-read substitution-only Fast Alignment Search Tool
bnelsj/mrssnake
Simple mrsfast read depth mapping using snakemake
bnelsj/pairsamtools
a legacy repo to avoid breaking existing pipelines
bnelsj/phylo-amp
Assessing model fit using posterior prediction
bnelsj/popFastaaa
Simple stand-alone programs for analysis of aligned Multi-FASTA formated files.
bnelsj/rd_custom_contig
Code for getting read depth-based copy number for a custom contig
bnelsj/segdup_phylogenetic_analysis
Pipeline based on phylogenetic methods in Sudmant et al. 2015 (SGDP)
bnelsj/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
bnelsj/ssf_DTS_caller
scale space filtering based CNV calling and genotyping
bnelsj/stream_read_pair
bnelsj/vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
bnelsj/vh_pipeline
Variation Hunter pipeline using snakemake
bnelsj/vst_calc
Calculate Vst statistics for populations
bnelsj/wssd_sunk
Legacy codebase for WSSD and SUNK read depth file creation and analysis
bnelsj/xhmm_pipeline
Snakemake pipeline for running XHMM