BOL: Related items

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Jit — Tue, 12 Jun 2018 08:14:41 -0500

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

BioJoker — Tue, 02 Apr 2019 21:54:55 -0500

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Rahul Nayak — Sat, 06 Jul 2019 03:48:22 -0500

Address of the bookmark: https://github.com/fenderglass/Flye

HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

Rahul Nayak — Tue, 08 May 2018 04:27:22 -0500

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

FastProNGS: fast preprocessing of next-generation sequencing reads

Rahul Nayak — Sat, 26 Dec 2020 08:35:21 -0600

FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.

Address of the bookmark: https://github.com/Megagenomics/FastProNGS

Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?

Rahul Agarwal — Wed, 17 Jul 2013 15:25:09 -0500

Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?

320000 viruses in mammals yet to sequenced in future!!!

Rahul Agarwal — Tue, 03 Sep 2013 08:35:30 -0500

With current biological technique improvements, finally it is now possible to look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, West Nile, Ebola, SARS, and influenza, are zoonoses - infections of animals that cross into humans.

To address the challenges of describing and estimating virodiversity, a team of investigators from Center for Infection and Immunity (CII) and EcoHealth Alliance began in jungles of Bangladesh - home to the flying fox.

Reference:

http://economictimes.indiatimes.com/news/news-by-industry/et-cetera/mammals-harbour-at-least-320000-new-viruses/articleshow/22253268.cms

http://www.bbc.co.uk/news/science-environment-23932400

npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

Shruti Paniwala — Mon, 11 Jun 2018 05:14:57 -0500

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.

Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

INC-Seq: accurate single molecule reads using nanopore sequencing

Jit — Mon, 27 Nov 2017 10:38:56 -0600

INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

Address of the bookmark: https://github.com/CSB5/INC-Seq

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

Rahul Nayak — Fri, 11 May 2018 05:07:45 -0500

MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 times faster than the current PBcR-Mhap pipeline. MECAT performance were compared with PBcR-Mhap pipeline, FALCON and Canu(v1.3) in five real datasets. The quality of assembled contigs produced by MECAT is the same or better than that of the PBcR-Mhap pipeline and FALCON.

https://www.nature.com/articles/nmeth.4432

Address of the bookmark: https://github.com/xiaochuanle/MECAT