BOL

https://pgapx.ybzhao.com/ - PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different...

github.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...

github.com - GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled...

https://proksee.ca/ - Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

madsalbertsen.github.io - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Mads...

github.com - This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a...

github.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...

github.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...

insilico.ehu.es - This tool allows to retrieve number of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophoresis (PFGE) is simulated. A tool for...

github.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...