bensutherland
genetics, genomics, gene expression, bioinformatics, open science
Sutherland BioinformaticsLantzville, British Columbia
Pinned Repositories
amplitools
Tools for working with amplicon sequencing data
assembly_metrics
Assess the results of a genome assembly through various metrics (e.g. N50, total length, BUSCO)
eDNA_metabarcoding
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
eRNA_taxo
A pipeline to conduct phylogenetics and functional transcriptomics on environmental DNA and RNA
fasta_SNP_extraction
Extract a section of a reference genome flanking an input locus with SNPs.
mate-pair_QC
to quality trim, bin by MP/PE/Unkn, align to ref, estimate insert size.
ms_oyster_popgen
Analysis of the Moore oyster project, Population Genomics
sfon_wgcna
Analysis of Brook Charr and Arctic Charr gene co-expression networks
simple_pop_stats
A short analysis of population statistics given specific inputs
Simple_reads_to_counts
From raw illumina reads data to counts
bensutherland's Repositories
bensutherland/eDNA_metabarcoding
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
bensutherland/simple_pop_stats
A short analysis of population statistics given specific inputs
bensutherland/assembly_metrics
Assess the results of a genome assembly through various metrics (e.g. N50, total length, BUSCO)
bensutherland/sfon_wgcna
Analysis of Brook Charr and Arctic Charr gene co-expression networks
bensutherland/Simple_reads_to_counts
From raw illumina reads data to counts
bensutherland/fasta_SNP_extraction
Extract a section of a reference genome flanking an input locus with SNPs.
bensutherland/amplitools
Tools for working with amplicon sequencing data
bensutherland/eRNA_taxo
A pipeline to conduct phylogenetics and functional transcriptomics on environmental DNA and RNA
bensutherland/mate-pair_QC
to quality trim, bin by MP/PE/Unkn, align to ref, estimate insert size.
bensutherland/ms_oyster_popgen
Analysis of the Moore oyster project, Population Genomics
bensutherland/overlappingReads
used as a pipeline to quality trim, then collapse overlapping reads (e.g. paired-end where insert size is less than the length of R1 + R2)
bensutherland/ms_oyster_panel
Repository for code to support the manuscript to design a Pacific oyster amplicon panel
bensutherland/nano2geno
Genotyping from nanopore data
bensutherland/2016_ms_sfonmap
Code required to collect data and analyze the high density S. fontinalis genetic map project.
bensutherland/2017_ms_immunostim
Associated code for analysis of 2017 manuscript immunostim
bensutherland/amplitargets
Target repository for panels designed and compatible with amplitools
bensutherland/bensutherland.github.io
bensutherland/coregonus_mapcomp
Collect and format Coregonus genetic map input data for MapComp analysis
bensutherland/hello_world
demo repo
bensutherland/ms_harbour_seal
Repository to accompany population genetics analysis of harbour seal manuscript.
bensutherland/ms_pike_popgen
A repository to accompany the analysis of the northern pike popgun study
bensutherland/ms_scallop_popgen
Repository to accompany scallop population genomics
bensutherland/poolparty
Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R
bensutherland/salp_anon_to_salp
Perform MapComp iteratively to attach anonymous Arctic Charr markers onto the Arctic Charr genetic map.
bensutherland/salp_anon_to_sfon
bensutherland/scotch_tape
A Poem for the Weekend
bensutherland/scripts
Various scripts
bensutherland/sfon_pqtl
Code associated with the sex chromosome, heterochiasmy and phenotypic QTL manuscript
bensutherland/SING_Canada_2018_genetics
Associated code for analysis of SING 2018 genetic data
bensutherland/stacks_workflow
RADseq workflow built around STACKS