Beast code in Giters

mrcardholder's starred repositories

maim

maim (make image) takes screenshots of your desktop. It has options to take only a region, and relies on slop to query for regions. maim is supposed to be an improved scrot.

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hyperloglog

HyperLogLog and HyperLogLog++ implementation in Go/Golang.

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genometools

GenomeTools genome analysis system.

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genomer

A Swiss army knife for genome projects

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genome

Python library and scripts for retrieval and storage of genomics data in HDF5 format

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RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

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cactus

Official home of genome aligner based upon notion of Cactus graphs

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fgwas

Functional genomics and genome-wide association studies

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genomego

Multi-threaded Genetic Algorithms library for Go.

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Sibelia

Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.

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velour

memory efficient short read de novo DNA sequence assembly tool for gigabase genomes

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gql

Genome query language

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genoset-norovirus

Determines if a genome is immune to norovirus (rs601338)

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dna2json

Formats your genome file as JSON

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fermi

A WGS de novo assembler based on the FMD-index for large genomes

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WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

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Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

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SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . Additionally the program provides the ability to model both site and base specific error, and scripts are provided to train this error model on real datasets. My hope in creating this program is to generate as realistic data as possible to assist in assessing the accuracy of genome assembly tools.

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jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

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genomesunzipped

Code for Genomes Unzipped

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trait-o-matic

An open-source tool to find and classify phenotypic correlations for variations in whole genomes. (For deployment, use the production branch.)

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RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.

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mrcardholder