cutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an...
http://meme-suite.org/ - Motif based sequence analysis suits
The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
The MEME Suite...
github.com - v0.0 by Glenn Hickey (hickey@soe.ucsc.edu)
Progressive Cactus is a whole-genome alignment package.
Requirements
git
gcc 4.2 or newer
python 2.7
wget
64bit processor and build environment
150GB+ of memory on at least one machine when...
chunlab.wordpress.com - CLgenomics is a standalone desktop software specifically designed for bacterial genome analysis. This program has a powerful multi-genome browser, which enables rapid and responsive exploration of bacterial genomes.
To use CLgenomics, individual...
To decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655
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...
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...
www.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...