njdbickhart Goto Github PK

annotateusinggenomicinfo

An annotation program I've written that can compare several data file types to UCSC data tracks.

bedutils

A collection of Java classes and abstractions to assist with processing bed files. Translates several algorithms from Aaron Quinlan's Bedtools to Java

bioinformaticstrainingworkshop

brahmanangusassemblyscripts

buffaloassemblyscripts

BuffaloAssemblyScripts

cattleassemblyscripts

Scripts and documentation related to the assembly of ARS-UCD1.2

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

checkbamlocs

A program that estimates depth of coverage over variant loci (BAM or VCF form)

combinefasta

A java utility to efficiently merge/order Fasta files

convertcufflinkstoexcel

Converts several cufflinks output files into easily readable excel tables using Apache's POI library

cosvard

Complementary Sequence Variant Detection

cosvardextensible

A java version of my sequence analysis automation pipeline

filetools

A catchall collection of Java classes and utilities that help to manage specialized file types

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

goatassemblyscripts

A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly

gridionpackageutils

A pipeline and group of scripts for managing GridION data

hh2manuscript

hpcvenvtutorial

Files used in a workshop describing how to set up virtual environments on the WUR HPC cluster

jarms

Java implementation of Mean Shift algorithm for RD CNV calling

jbwa

Java Bindings (JNI) for bwa

jmrsfast

A Java port of the MrsFAST-Ultra algorithm for rapid mapping location discovery

labnotes

A listing of the commands, protocols and other notes that I take on a daily basis

largevcfparser

Parsing utility for larger, multi-sample VCF files

lowesssmoother

Method to normalize genomic window values by locally weighted linear regression of GC% values

magpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)

meidivetid

Finds MEI from divet files

meryl

A genomic k-mer counter (and sequence utility) with nice features.