BOL

github.com - A program to detect recombination hotspots using population genetic data. More at https://github.com/auton1/LDhot

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...

journals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...

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...

http://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...

github.com - A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

www.atgc.org - PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements....

github.com - MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different...

FASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...

github.com - FQC is software that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsing results, and aggregating quality metrics into an interactive dashboard designed to richly summarize individual sequencing runs. The...