BOL: Related items

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

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

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

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/

Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore

Neel — Fri, 19 Oct 2018 08:48:43 -0500

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy.

Address of the bookmark: https://github.com/ruanjue/wtdbg2

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

MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s)

Jit — Tue, 12 Dec 2017 17:23:31 -0600

MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It does not compute the alignments explicitly, but rather estimates a k-mer based Jaccard similarity using a combination of Winnowing and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined given minimum local alignment length and identity thresholds. The efficiency of the algorithm improves as both of these thresholds are increased.

Address of the bookmark: https://github.com/marbl/MashMap

LoRMA: A tool for correcting sequencing errors in long reads

Abhimanyu Singh — Thu, 06 Sep 2018 16:21:01 -0500

An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

CoLoRMap: Correcting Long Reads by Mapping short reads

Jit — Mon, 20 Aug 2018 14:17:05 -0500

Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage. This motivates the development of hybrid approaches that leverage the high quality of short reads to correct errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping short reads that minimizes the edit score to a long read and extending corrected regions by local assembly of unmapped mates of mapped short reads. Our results on bacterial, fungal and insect data sets show that CoLoRMap compares well with existing hybrid correction methods.The source code of CoLoRMap is freely available for non-commercial use at https://github.com/sfu-compbio/colormap

ehaghshe@sfu.ca or cedric.chauve@sfu.ca

Address of the bookmark: https://github.com/sfu-compbio/colormap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

Jit — Wed, 07 Jun 2017 04:18:16 -0500

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html

Features

    Mapping position agnostic to alignment parameters.
    Consistently very high sensitivity and precision across different error profiles, rates and sequencing technologies even with default parameters.
    Circular genome handling to resolve coverage drops near ends of the genome.
    E-value.
    Meaningful mapping quality.
    Various alignment strategies (semiglobal bit-vector and Gotoh, anchored).
    Overlapping of reads for de novo assembly.
    Transcriptome mapping through internal construction of a transcriptome from a given genomic reference and a GTF file.
    ...and much more.

GraphMap is also used as an overlapper in a new de novo genome assembly project called Ra (https://github.com/mariokostelac/ra-integrate).
Ra attempts to create de novo assemblies from raw nanopore and PacBio reads without requiring error correction, for which a highly sensitive overlapper is required.

Currently, development of a new spliced-alignment mode for mapping RNA-seq reads is under way.
Description of the current effort as well as how to reach the experimental implementation can be found here: doc/rnaseq.md.

Address of the bookmark: https://github.com/isovic/graphmap