bensutherland Goto Github PK

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

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)

bensutherland.github.io

coregonus_mapcomp

Collect and format Coregonus genetic map input data for MapComp analysis

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.

genomesubsetassemble

Used to map trimmed reads against a genome, subset for those mapping to specific contig/scaffold and prepare for assembly

hello_world

demo repo

mate-pair_qc

to quality trim, bin by MP/PE/Unkn, align to ref, estimate insert size.

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_oyster_popgen

Analysis of the Moore oyster project, Population Genomics

ms_pike_popgen

A repository to accompany the analysis of the northern pike popgun study

ms_scallop_popgen

Repository to accompany scallop population genomics

nano2geno

Genotyping from nanopore data

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)

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.

salp_anon_to_sfon

scotch_tape

A Poem for the Weekend

scripts

Various scripts

sfon_pqtl

Code associated with the sex chromosome, heterochiasmy and phenotypic QTL manuscript

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

sing_canada_2018_genetics

Associated code for analysis of SING 2018 genetic data