Derek Bickhart's repositories
GoatAssemblyScripts
A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
SheepHiFiManuscript
A collection of scripts and workflows to analyze HiFi assembled metagenomes
python_toolchain
A collection of my python 3 scripts and programs
Themis-ASM
A genome assembly comparison pipeline using comparative alignment statistics
CombineFasta
A java utility to efficiently merge/order Fasta files
CattleAssemblyScripts
Scripts and documentation related to the assembly of ARS-UCD1.2
GridIONPackageUtils
A pipeline and group of scripts for managing GridION data
LargeVCFParser
Parsing utility for larger, multi-sample VCF files
perl_toolchain
Backup for my personal perl scripts
RumenLongReadASM
Scripts, notes and commands to accompany our Rumen Metagenome assembly manuscript
BuffaloAssemblyScripts
BuffaloAssemblyScripts
CDCBConflictTranslator
Translator for CDCB codes from csv files
cdcbConsolidator
A GUI tool to consolidate CDCB files
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
ForageAssemblyScripts
Scripts and tools to assist with the genome assembly of plant forage species
GetMaskBedFasta
A program that efficiently identifies masked or gap regions in assemblies
HPCVEnvTutorial
Files used in a workshop describing how to set up virtual environments on the WUR HPC cluster
njdbickhart.github.io
Bovine Pan-Genome Consortium Website
ObjectUtils
A personal library for manipulating collections, enumerated sets and the like
pseudohaploid
Create a pseudohaploid assembly from a partially resolved diploid assembly
ResolveKmerGraph
A tool to use heterozygous kmers to resolve read origins