BOL

github.com - Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., & Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (publication link) Mitofinder is a pipeline to assemble mitochondrial 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)...

rrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...

mitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...

journals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAP

https://dfast.nig.ac.jp/ - We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its...

sanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...

github.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...

maq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....

bioinformatics.oxfordjournals.org - Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a...