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

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

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

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/

Swabs to Genomes: A Comprehensive Workflow

Rahul Nayak — Sun, 10 Aug 2014 03:01:21 -0500

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Address of the bookmark: https://peerj.com/preprints/453.pdf

deepTools

Martin Jones — Sat, 08 Nov 2014 15:02:08 -0600

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

Rosalind Bioinformatics problems !!!

Abhi — Thu, 18 Dec 2014 10:32:48 -0600

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

LASTZ

Abhi — Mon, 18 Apr 2016 04:41:55 -0500

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

Rosalind Problem Solution with Perl

Jit — Tue, 09 Jun 2015 23:35:18 -0500

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

Bioinformatics Textbook Track

Find more about Rosalind puzzle at http://rosalind.info/problems/list-view/?location=bioinformatics-textbook-track

I will provide solution of all the Rosalind problem with Perl for community.

Check out the right sidebar for more links ...

Research Associate MANIT - Allahabad, Uttar Pradesh

Fri, 12 Jun 2015 05:44:38 -0500

Applications are invited from Indian nationals for the post of Research Assistant (on contract) in research project entitled “Identification of novel drug targets in Aspergillus fumigatus genome prioritized by essentiality based screening and rational designing of new antifungal compounds” sanction order no. CST/238 dated 12/05/2015 sponsored by Council of Science and Technology U.P.

The duly completed application on prescribed format along with copies of supporting documents must reach to: Office of the Dean (Research & Consultancy), Motilal Nehru National Institute of Technology, Allahabad-211004 on or before 03/07/2015.

The position is purely temporary and will be governed by the funding agency rules & service conditions of Office of the Dean (Research & Consultancy), MNNIT Allahabad.

For detail advertisement see: www.mnnit.ac.in/images/newstories/Advertisement_for_the_post_of_Research_Assistant_in_UPCST_Project_of_Biotechnology_Department.pdf