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github.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...

academic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...

ufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...

www.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...

In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.

github.com - Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). It can assemble a human genome from 30x reads within 20 cpu hours from reads to polished consensus. It uses Sparse HIereachical MimiMizER (SHIMMER)...

github.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...

omega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...

github.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...

github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...