Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish stats" command. See the documentation below for more details.

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joshuaburkhart/BoreKit

scripts to assist with the TORQUE Resource Manager

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joshuaburkhart/RadiQual

a project to assess genome assembly quality using RAD sequence alignment

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joshuaburkhart/screed

a simple read-only sequence database, designed for short reads

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joshuaburkhart/khmer

in-memory k-mer counting

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joshuaburkhart/planet_lab

files for use with PlanetLab, a group of computers available as a testbed for computer networking and distributed systems research

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joshuaburkhart/psshim

pssh improved

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joshuaburkhart/bio

software to support various bioinformatics research tasks

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joshuaburkhart/FRC_align

Computes FRC from SAM/BAM file and not from afg files

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joshuaburkhart/super_qmon

an application for mobile devices that allows one to monitor their queued TORQUE Resource Manager batch jobs

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joshuaburkhart/cdn_mon

a project to collect and aggregate metrics and conducts analysis on modern content delivery networks

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joshuaburkhart/wiggle_dbc

a tool that finds density-based signal clusters in wiggle files that can be displayed using the UCSC Genome Browser

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joshuaburkhart/CIS_211

code to accompany University of Oregon's CIS 211 Spring Term, 2012

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joshuaburkhart/CIS_553

A repository for code used in CIS 553 assignments

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joshuaburkhart/Lab_Usage

software to monitor lab computer usage

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joshuaburkhart/laplace

The goals of this assignment are to gain some experience with another important class of computational science applications (PDE solvers) and to write a non-trivial program using OpenMP.

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joshuaburkhart/air_13_config

Configuration files for my MacBook Air. The new MacBook Air is faster and more powerful than before, yet it's still incredibly thin and light. It's everything a notebook should be. And more.

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joshuaburkhart/plbm

CIS 555 term project to create a program capable of phylogenetic bipartite linear modeling

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joshuaburkhart/N-Body

This project involves the implementation of a straightforward O(n^2) n-body simulation. The distribution contains the outline of a sequential simulator and data based on the sun and nine planets in the solar system to test the simulator.

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