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python_toolchain Public
A collection of my python 3 scripts and programs
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labnotes Public
A listing of the commands, protocols and other notes that I take on a daily basis
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HPCVEnvTutorial Public
Files used in a workshop describing how to set up virtual environments on the WUR HPC cluster
Shell UpdatedJul 24, 2023 -
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ForageAssemblyScripts Public
Scripts and tools to assist with the genome assembly of plant forage species
Perl MIT License UpdatedFeb 9, 2022 -
Themis-ASM Public
A genome assembly comparison pipeline using comparative alignment statistics
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GetMaskBedFasta Public
A program that efficiently identifies masked or gap regions in assemblies
Java UpdatedJan 28, 2022 -
CombineFasta Public
A java utility to efficiently merge/order Fasta files
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SheepHiFiManuscript Public
A collection of scripts and workflows to analyze HiFi assembled metagenomes
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cDNA_Cupcake Public
Forked from Magdoll/cDNA_CupcakeMiscellaneous collection of Python and R scripts for processing Iso-Seq data
Python BSD 3-Clause Clear License UpdatedDec 17, 2020 -
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meryl Public
Forked from marbl/merylA genomic k-mer counter (and sequence utility) with nice features.
C UpdatedSep 29, 2020 -
njdbickhart.github.io Public
Forked from daattali/beautiful-jekyllBovine Pan-Genome Consortium Website
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RumenLongReadASM Public
Scripts, notes and commands to accompany our Rumen Metagenome assembly manuscript
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CattleAssemblyScripts Public
Scripts and documentation related to the assembly of ARS-UCD1.2
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BioinformaticsTrainingWorkshop Public
Forked from haibol2016/BioinformaticsTrainingWorkshopUpdatedJan 6, 2020 -
ResolveKmerGraph Public
A tool to use heterozygous kmers to resolve read origins
Java UpdatedNov 14, 2019 -
MAGpy Public
Forked from WatsonLab/MAGpySnakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
Python UpdatedNov 7, 2019 -
GridIONPackageUtils Public
A pipeline and group of scripts for managing GridION data
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pseudohaploid Public
Forked from schatzlab/pseudohaploidCreate a pseudohaploid assembly from a partially resolved diploid assembly
Perl UpdatedOct 2, 2019 -
BrahmanAngusAssemblyScripts Public
Forked from lloydlow/BrahmanAngusAssemblyScriptsR UpdatedAug 7, 2019 -
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JaRMS Public
Java implementation of Mean Shift algorithm for RD CNV calling
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BuffaloAssemblyScripts Public
Forked from lloydlow/BuffaloAssemblyScriptsBuffaloAssemblyScripts
R UpdatedJul 27, 2018 -
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ObjectUtils Public
A personal library for manipulating collections, enumerated sets and the like
Java UpdatedDec 12, 2017 -
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LargeVCFParser Public
Parsing utility for larger, multi-sample VCF files
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GoatAssemblyScripts Public
A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly
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RAPTR-SV Public
RAPTR-SV uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data