Ben Sutherland's repositories
eDNA_metabarcoding
Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
simple_pop_stats
A short analysis of population statistics given specific inputs
assembly_metrics
Assess the results of a genome assembly through various metrics (e.g. N50, total length, BUSCO)
sfon_wgcna
Analysis of Brook Charr and Arctic Charr gene co-expression networks
Simple_reads_to_counts
From raw illumina reads data to counts
fasta_SNP_extraction
Extract a section of a reference genome flanking an input locus with SNPs.
amplitools
Tools for working with amplicon sequencing data
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
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)
2016_ms_sfonmap
Code required to collect data and analyze the high density S. fontinalis genetic map project.
2017_ms_immunostim
Associated code for analysis of 2017 manuscript immunostim
amplitargets
Target repository for panels designed and compatible with amplitools
coregonus_mapcomp
Collect and format Coregonus genetic map input data for MapComp analysis
hello_world
demo repo
ms_harbour_seal
Repository to accompany population genetics analysis of harbour seal manuscript.
ms_oyster_panel
Repository for code to support the manuscript to design a Pacific oyster amplicon panel
ms_pike_popgen
A repository to accompany the analysis of the northern pike popgun study
ms_scallop_popgen
Repository to accompany scallop population genomics
poolparty
Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R
salp_anon_to_salp
Perform MapComp iteratively to attach anonymous Arctic Charr markers onto the Arctic Charr genetic map.
scotch_tape
A Poem for the Weekend
SING_Canada_2018_genetics
Associated code for analysis of SING 2018 genetic data
stacks_workflow
RADseq workflow built around STACKS