BOL: Related items

1mb long DNA with Nanopore technology

Jit — Tue, 19 Dec 2017 18:49:28 -0600

The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

BioStar — Tue, 04 Feb 2020 23:23:16 -0600

Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.

Usage: perl run_rcorrector.pl [OPTIONS]
OPTIONS:
	Required
	-s seq_files: comma separated files for single-end data sets
	-1 seq_files_left: comma separated files for the first mate in the paried-end data sets
	-2 seq_files_right: comma separated files for the second mate in the paired-end data sets
	-i seq_files_interleaved: comma sperated files for interleaved paired-end data sets
	Optional
	-k INT: kmer_length (<=32, default: 23)
	-od STRING: output_file_directory (default: ./)
	-t INT: number of threads to use (default: 1)
	-trim : allow trimming (default: false)
	-maxcorK INT: the maximum number of correction within k-bp window (default: 4)
	-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
	-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
	-stdout: output the corrected reads to stdout (default: not used)
	-verbose: output some correction information to stdout (default: not used)
	-stage INT: start from which stage (default: 0)
		0-start from begining(storing kmers in bloom filter) ;
		1-start from count kmers showed up in bloom filter;
		2-start from dumping kmer counts into a jf_dump file;
		3-start from error correction.

Address of the bookmark: https://github.com/mourisl/Rcorrector/

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

Rahul Nayak — Thu, 14 May 2020 15:09:52 -0500

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

BASE: a practical de novo assembler for large genomes using long NGS reads

Rahul Nayak — Fri, 19 Oct 2018 07:25:21 -0500

new de novo assembler called BASE. It enhances the classic seed-extension approach by indexing the reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to use reverse validation to remove the branches based on read coverage and paired-end information, resulting in high-quality consensus sequences of reads sharing the seeds. Such consensus sequences are then extended to contigs.

Address of the bookmark: https://github.com/dhlbh/BASE

Evaluation of genome assembly software based on long reads

BioStar — Fri, 01 Feb 2019 11:55:54 -0600

TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome.

In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads

HASLR: a tool for rapid genome assembly of long sequencing reads

LEGE — Fri, 31 Jan 2020 05:50:15 -0600

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample.

Address of the bookmark: https://github.com/vpc-ccg/haslr

LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

LEGE — Fri, 17 Sep 2021 01:57:02 -0500

The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating efficiency, diversified classification and interactive analysis report. LncPipe allows users additional control in interuppting the pipeline, resetting parameters from command line, modifying main script directly and resume analysis from previous checkpoint.

Ref https://www.lncrnablog.com/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data/

Address of the bookmark: https://github.com/likelet/LncPipe

IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer

Jit — Thu, 23 Nov 2017 10:24:19 -0600

This package is intended to provide tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer. It includes a functions to generate a number plots for examining the statistics that we think will be useful for this task.

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html

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