BOL: Related items

HALC: High throughput algorithm for long read error correction

Jit — Fri, 08 Jun 2018 10:47:41 -0500

HALC, a high throughput algorithm for long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long read region can be aligned to at least one contig region, including its true genome region’s repeats in the contigs sufficiently similar to it (similar repeat based alignment approach) HALC was able to obtain 6.7-41.1% higher throughput than the existing algorithms while maintaining comparable accuracy. The HALC corrected long reads can thus result in 11.4-60.7% longer assembled contigs than the existing algorithms.

Address of the bookmark: https://github.com/lanl001/halc

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

Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

BioStar — Mon, 12 Nov 2018 05:26:48 -0600

Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf.

The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

Shasta long read assembler

Jit — Tue, 14 Jan 2020 06:47:07 -0600

The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.

Computational methods used by the Shasta assembler include:

Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads.
Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10).

More at https://chanzuckerberg.github.io/shasta/index.html

Address of the bookmark: https://github.com/chanzuckerberg/shasta

LRCstats: Long Read Correction Statistics

Jit — Fri, 05 Jan 2018 04:04:20 -0600

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are longer in length than reads produced by next generation sequencing technologies, such as those produced by Illumina. However, long reads are plagued by high error rates, which can cause issues in downstream analysis. Long read correction algorithms reduce the error rate of long reads either through self-correcting methods or using accurate, short reads outputted by next generation sequencing technologies to correct long reads.

Of course, some long read correction algorithms are better than others, and developers of long read correction algorithms will wish to compare their algorithm with others currently available. LRCstats benchmarks long read correction algorithms using long reads produced by simulators (such as SimLoRD or PBSim) where the two-way alignments between the uncorrected long reads (uLR) and the corresponding sequences in the reference genome (Ref) are given in some sort of alignment file and then aligning the corrected long reads (cLR) to the Ref-uLR two-way alignments to create three-way alignments using a dynamic programming algorithm. Statistics on these three-way alignments are then collected, such as the overall error rates of the corrected long reads.

https://www.healthcare.uiowa.edu/labs/au/LSC/

Address of the bookmark: https://github.com/cchauve/lrcstats

LSC: Improving PacBio Long Read Accuracy by Short Read Alignment

Abhimanyu Singh — Thu, 06 Sep 2018 16:27:35 -0500

Added Command line argument support.
Multi-stage execution modes.
Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
Better compressed intermediate files.
Added utilities folder.
Added support for multiple short read files.
Removed use of configuration file.

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

BioJoker — Tue, 27 Nov 2018 04:43:57 -0600

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

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

GAM-NGS: genomic assemblies merger for next generation sequencing

Jit — Fri, 19 May 2017 07:44:14 -0500

GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20 available assemblers it is hard to select the best tool. In this context we propose a tool that improves assemblies (and, as a by-product, perhaps even assemblers) by merging them and selecting the generating that is most likely to be correct.

Address of the bookmark: https://github.com/vice87/gam-ngs