BOL

github.com - Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into...

github.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...

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)...

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...

http://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...

majiq.biociphers.org -   Ability to detect, quantify, and visualize complex and de-novo splicing variations from RNASeq. MAJIQ’s accuracy compares favorably to other algorithms. MAJIQ 2 is *way* faster, more memory and I/O efficient New visualization (VOILA...

rgraphgallery.blogspot.be - The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided....

www.ncbi.nlm.nih.gov - VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and...

github.com - This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining...