BOL

sourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...

bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...

amos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...

blobtoolkit.genomehubs.org - Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible...

training.galaxyproject.org - In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull...

If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...

lh3.github.io - Given a de novo assembly, we often measure the “average” contig length by N50. N50 is neither the real average nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the assembly. A...

Mitochondrial genome assembly tools are specialized software and algorithms designed to accurately reconstruct the mitochondrial genome (mitogenome) from sequencing data, typically obtained through techniques like next-generation sequencing (NGS)....

https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...

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...