Bioinformatics

CNVpytor

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.

CONCOCT

A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

Core-genome-alignment

Scripts to make a concatenated alignment of core genes from bacterial genomes and compare gene content.

Corona Lite

Corona Lite is a genome alignment tool.

Cufflinks

Cufflinks is a reference-guided assembler for RNA-Seq experiments. It simultaneously assembles transcripts from reads and estimates their relative abundances, without using a reference annotation.

DAS Tool

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

dDocent

dDocent was designed as a scripted software pipeline made for analyzing double digest RAD (Peterson et al. 2012) or ezRAD (Toonen et al. 2013) data in highly polymorphic marine species.

Dextractor

The Dextractor commands allow one to pull exactly and only the information needed for assembly and reconstruction from the source HDF5 files produced by the PacBio RS II sequencer, or from the source BAM files produced by the PacBio Sequel sequencer.

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