BOL

Integrated solutions CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...

http://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...

www.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...

github.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...

Brief Overview of Snakemake Pipeline Commands

github.com - YAMP is constructed on Nextflow, a framework based on the dataflow programming model, which allows writing workflows that are highly parallel, easily portable (including on distributed systems), and very flexible and customisable,...

github.com - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs...

nservant.github.io - HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...

github.com - An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to...

tritexassembly.bitbucket.io - The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable...