Pinned Repositories
BedUtils
A collection of Java classes and abstractions to assist with processing bed files. Translates several algorithms from Aaron Quinlan's Bedtools to Java
CattleAssemblyScripts
Scripts and documentation related to the assembly of ARS-UCD1.2
CombineFasta
A java utility to efficiently merge/order Fasta files
GoatAssemblyScripts
A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
JaRMS
Java implementation of Mean Shift algorithm for RD CNV calling
labnotes
A listing of the commands, protocols and other notes that I take on a daily basis
python_toolchain
A collection of my python 3 scripts and programs
RAPTR-SV
RAPTR-SV uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data
SheepHiFiManuscript
A collection of scripts and workflows to analyze HiFi assembled metagenomes
Themis-ASM
A genome assembly comparison pipeline using comparative alignment statistics
njdbickhart's Repositories
njdbickhart/GoatAssemblyScripts
A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
njdbickhart/labnotes
A listing of the commands, protocols and other notes that I take on a daily basis
njdbickhart/RAPTR-SV
RAPTR-SV uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data
njdbickhart/SheepHiFiManuscript
A collection of scripts and workflows to analyze HiFi assembled metagenomes
njdbickhart/python_toolchain
A collection of my python 3 scripts and programs
njdbickhart/Themis-ASM
A genome assembly comparison pipeline using comparative alignment statistics
njdbickhart/CombineFasta
A java utility to efficiently merge/order Fasta files
njdbickhart/JaRMS
Java implementation of Mean Shift algorithm for RD CNV calling
njdbickhart/CattleAssemblyScripts
Scripts and documentation related to the assembly of ARS-UCD1.2
njdbickhart/GridIONPackageUtils
A pipeline and group of scripts for managing GridION data
njdbickhart/HH2Manuscript
njdbickhart/LargeVCFParser
Parsing utility for larger, multi-sample VCF files
njdbickhart/perl_toolchain
Backup for my personal perl scripts
njdbickhart/RumenLongReadASM
Scripts, notes and commands to accompany our Rumen Metagenome assembly manuscript
njdbickhart/BioinformaticsTrainingWorkshop
njdbickhart/BrahmanAngusAssemblyScripts
njdbickhart/BuffaloAssemblyScripts
BuffaloAssemblyScripts
njdbickhart/CDCBConflictTranslator
Translator for CDCB codes from csv files
njdbickhart/cdcbConsolidator
A GUI tool to consolidate CDCB files
njdbickhart/cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
njdbickhart/ForageAssemblyScripts
Scripts and tools to assist with the genome assembly of plant forage species
njdbickhart/GetMaskBedFasta
A program that efficiently identifies masked or gap regions in assemblies
njdbickhart/HPCVEnvTutorial
Files used in a workshop describing how to set up virtual environments on the WUR HPC cluster
njdbickhart/MAGpy
Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
njdbickhart/meryl
A genomic k-mer counter (and sequence utility) with nice features.
njdbickhart/njdbickhart.github.io
Bovine Pan-Genome Consortium Website
njdbickhart/ObjectUtils
A personal library for manipulating collections, enumerated sets and the like
njdbickhart/pseudohaploid
Create a pseudohaploid assembly from a partially resolved diploid assembly
njdbickhart/ResolveKmerGraph
A tool to use heterozygous kmers to resolve read origins
njdbickhart/SIFF
Interrogate, reformat and validate assembly fasta files