BOL: Related items

MEC: Contig Misassembly Correction

BioStar — Tue, 04 Feb 2020 23:40:49 -0600

MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the statistical analysis of GC-contents. We apply MEC to four real contig datasets, and carry out experiments to analyze the influence of MEC on scaffolding results, which shows that MEC can reduce misassemblies effectively and result in quantitative improvements in scaffolding quality. MEC is publicly available for download at https://github.com/bioinfomaticsCSU/MEC.

Address of the bookmark: https://github.com/bioinfomaticsCSU/MEC

NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads

BioStar — Thu, 24 Jan 2019 10:35:12 -0600

NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, unaffected contigs.

https://nxrepair.readthedocs.io/en/latest/tutorial.html

nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new_fasta.fasta

Address of the bookmark: https://github.com/rebeccaroisin/nxrepair

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

Strand — Tue, 04 Aug 2015 05:14:07 -0500

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore

Jit — Wed, 25 Apr 2018 07:30:54 -0500

CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).

Address of the bookmark: https://github.com/philres/ngmlr

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

Jit — Tue, 22 Jan 2019 06:26:55 -0600

Run a pipeline processing fast5s to a consensus in a single command.
Recommended fixed "standard" and "fast" pipelines.
Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
Seemless distribution of tasks over local or distributed compute.
Highly configurable.
Open source (Mozilla Public License 2.0).

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

Cerulean: A hybrid assembly using high throughput short and long reads

Rahul Nayak — Tue, 05 Jun 2018 10:10:15 -0500

Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (2013). Cerulean: A hybrid assembly using high throughput short and long reads. arXiv preprint arXiv:1307.7933. http://arxiv.org/abs/1307.7933

Address of the bookmark: https://sourceforge.net/projects/ceruleanassembler/

ONT assembly and Illumina polishing pipeline

Jit — Thu, 23 Nov 2017 10:13:42 -0600

This pipeline performs the following steps:

Assembly of nanopore reads using Canu.
Polish canu contigs using racon (optional).
Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

rHAT: a seed-and-extension-based noisy long read alignment tool

Abhimanyu Singh — Sun, 23 Sep 2018 05:12:22 -0500

rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.

Address of the bookmark: https://github.com/dfguan/rHAT

DNA Bending Propensity in the Presence of Base Mismatches: Implications for DNA Repair

Jitendra Narayan — Mon, 19 Aug 2013 16:01:44 -0500

Understanding how the human body recognizes damaged DNA and initiates repair fascinates Michael Feig, professor of biochemistry and molecular biology at Michigan State University. Feig studies the proteins MutS and MSH2-MSH6, which recognize defective DNA and initiate DNA repair. Natural DNA repair occurs when proteins like MutS (the primary protein responsible for recognizing a variety of DNA mismatches) scan the DNA, identify a defect, and recruit other enzymes to carry out the actual repair.

Results from computer simulations show that it is energetically less expensive to bend mismatch-containing, defective DNA (G:T, C:C, C:T, G:A, G:G, T:T, A:A, A+:C) vs. non-defective DNA (containing A:T or G:C base pairs). DNA repair mechanisms likely take advantage of this feature to detect defective DNA based on an increased bending propensity.

http://www.tacc.utexas.edu/news/feature-stories/2013/how-dna-repair-helps-prevent-cancer

http://pubs.acs.org/doi/abs/10.1021/jp403127a