BOL: Related items

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

Rahul Nayak — Fri, 19 Oct 2018 08:23:42 -0500

Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top–down manner. And along a guided tree, it iteratively merges sibling leaves in a bottom–up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data

Address of the bookmark: https://sourceforge.net/projects/bio-rainbow/files/

Vital-IT

Abhi — Thu, 18 Dec 2014 10:46:59 -0600

Vital-IT is a bioinformatics competence center that supports and collaborates with life scientists in Switzerland and beyond. The multi-disciplinary team provides expertise, training and maintains a high-performance computing (HPC) and storage infrastructure, so as to help develop, maintain and extend life science and medical research (activities).

Address of the bookmark: http://www.vital-it.ch/

Genome assembly tutorial "Genome Assembly for short and long reads"

Jit — Sat, 19 Jan 2019 17:29:53 -0600

In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will know:

How to perform basic quality checks on the input data
How to run a short read assembler on Illumina data
How to run a long read assembler on Pacific Biosciences or Oxford Nanopore data
How to improve the accuracy of a long read assembly using short reads
How to assess the quality of an assembly

https://bioinformaticsdotca.github.io/high-throughput_biology_2017

Address of the bookmark: https://bioinformaticsdotca.github.io/high-throughput_biology_2017_module6_lab

NextDenovo: string graph-based de novo assembler for TGS long reads

Jit — Sun, 05 Jan 2020 04:08:29 -0600

NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly less computing resources and storages. After assembly, the per-base error rate is about 97-98%, to further improve single base accuracy, please use NextPolish.

NextDenovo contains two core modules: NextCorrect and NextGraph. NextCorrect can be used to correct TGS long reads with approximately 15% sequencing errors, and NextGraph can be used to construct a string graph with corrected reads. It also contains a modified version of minimap2 for adapting input and output and producing more sensitive and accurate dovetail overlaps, and some useful utilities (see here for more details).

Address of the bookmark: https://github.com/Nextomics/NextDenovo

Bioinformatics Scientist at ICAR Labs

Sun, 21 Dec 2014 23:47:03 -0600

AGRICUL AGRICULTURAL SCIENTISTS RECRUITMENT BOARD TURAL SCIENTISTS RECRUITMENT BOARD
KRISHI ANUSANDHAN BHAVAN-I, PUSA, NEW DELHI-110 012

ADVERTISEMENT NO. 03/2014

PRINCIPAL SCIENTIST

Pay Band: Minimum pay of `43,000 in the PB-4 of `37400-67000/- + RGP of `10,000/-.

Age: The candidates must not have attained the age of 52 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

ICAR-Indian Institute for Agricultural Biotechnology, (IIAB) Ranchi (Jharkhand)

151. Principal Scientist (Bioinformatics) (One post)

SENIOR SCIENTIST/PROGRAMME COORDINATOR

Pay Band: PB-4 of ` 37400-67000/- + RGP of ` 9,000/-.

Age: The candidates must not have attained the age of 47 years as on 19.01.2015. There shall be no age limit for the Council’s employees.

National Institute of Biotic Stress Management, Raipur (Chhattishgarh)

166. Senior Scientist (Bioinformatics) (One post)

IMPORTANT NOTE
I. (i) CLOSING DATE

THE CLOSING DATE FOR RECEIPT OF APPLICATIONS IN AGRICULTURAL SCIENTISTS RECRUITMENT BOARD IS 19.01.2015 (For applications posted from abroad and in the Andaman and Nicobar Islands, Lakshdweep, Minicoy and Amindivi islands, States/ Union Territories in the North-Eastern Region, Ladakh Division of J & K State, Sikkim, Pangi, Sub-division of Chamba, Lahul and Spiti Districts of Himachal Pradesh, the last date for receipt of application will be 02.02.2015). Non receipt of the application by the closing date will result in rejection of the application.

More Info: http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf

Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads

Jit — Mon, 10 Feb 2020 02:45:53 -0600

Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.

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

ShRec3D

Jitendra Narayan — Thu, 25 Dec 2014 23:14:52 -0600

ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776).

There are two options to run ShRec3D (on linuX only so far): the first one uses the Matlab complier runtime environment (MCR), the second one doesn't need any other library to be installed but only works with the latest versions of Linux (equivalent to Fedora 19 and above).

Address of the bookmark: https://sites.google.com/site/julienmozziconacci/#TOC-Downloads

Filtlong: quality filtering tool for long reads

Radha Agarkar — Wed, 13 May 2020 10:23:55 -0500

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

Filtlong builds into a stand-alone executable:

git clone https://github.com/rrwick/Filtlong.git
cd Filtlong
make -j
bin/filtlong -h

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

Which of the followings are the best place to study Bioinformatics ?

Reshma Khatun — Sun, 28 Dec 2014 00:20:30 -0600

Bioinformatics is a major growth area and qualified Bioinformaticians are in high demand. An explosion in biological data has resulted from genome projects, next generation sequencing and other 'omics' techniques. Bioinformatics provides the tools to analyse and exploit such data sets.

Can you please suggest me the best place to study bioinformatics ( Grad/PostGrad).

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Jit — Thu, 24 Dec 2020 10:03:36 -0600

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.

Address of the bookmark: https://github.com/chhylp123/hifiasm