cpansearch.perl.org - This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The...
homer.salk.edu - This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER.
Setting up your computing environment
Retrieving and storing...
drive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW.
UPARSE >OTU clustering for 16S and other marker genes....
github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly.
More at...
github.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...
bioen-compbio.bioen.illinois.edu - Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end...
engr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...
www.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...
github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.
Canu is...
www.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...