BOL

github.com - LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...

github.com - Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are...

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...

github.com - HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering.  More...

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...

compbio.cs.toronto.edu - PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with...

github.com - pyScaf orders contigs from genome assemblies utilising several types of information: paired-end (PE) and/or mate-pair libraries (NGS-based mode) long reads (NGS-based mode) synteny to the genome of some related species (reference-based...

www.cbcb.umd.edu - Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with...

github.com - GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two...