Neel
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Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2694 days ago Comments (1)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...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2687 days agoamos.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,...3D de novo assembly (3D DNA) pipeline
By Jit 2315 days agogithub.com - For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the...BlobToolKit: A toolkit for genome assembly QC
By Jit 2297 days agoblobtoolkit.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...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2226 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...liftover
By Jitendra Narayan 3770 days ago Comments (1)github.com - Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3692 days ago Comments (2)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...Redundans
By Jit 3564 days agogithub.com - Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should...Standardized velvet assembly report
By Poonam Mahapatra 3465 days agogithub.com - Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate...ScaffMatch
By Jit 3461 days agoalan.cs.gsu.edu - caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one...
