BOL: Related items

Understanding HiFi Reads !

Rahul Nayak — Thu, 24 Mar 2022 19:48:11 -0500

While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot presented (below), synthetic Infinity reads – labeled “Longas” – are at the top, followed by standard Illumina short reads, and PacBio HiFi reads labeled “CCS” depicted at the bottom:

Address of the bookmark: http://pacb.com/blog/the-hifi-difference-true-long-reads-vs-synthetic-long-reads/

List of bioinformatics workflow management tools !

Rahul Nayak — Sat, 20 Mar 2021 00:15:25 -0500

Here are list of Workflow Managers

BigDataScript – A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
Bpipe – A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
Common Workflow Language – a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
Cromwell – A Workflow Management System geared towards scientific workflows. [ web ]
Galaxy – a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
Nextflow (recommended) – A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
Ruffus – Computation Pipeline library for python widely used in science and bioinformatics. [ paper-2010 | web ]
SeqWare – Hadoop Oozie-based workflow system focused on genomics data analysis in cloud environments. [ paper-2010 | web ]
Snakemake – A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Workflow Descriptor Language – Workflow standard developed by the Broad. [ web ]

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

ngs-bits - Short-read sequencing tools

Neel — Thu, 16 Jan 2020 23:14:00 -0600

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

Perl Maven tutorial by Gabor Szabo

Jitendra Narayan — Fri, 09 Aug 2013 05:43:10 -0500

I personally reccoment this tutorial for Perl users.

More detail http://perlmaven.com/

Cava Deployment Tools

Jitendra Narayan — Wed, 14 Aug 2013 15:00:48 -0500

Cava Packager allows packaging of applications written in Perl. Packaged applications can be distributed without the need for an installation of Perl on the target machine. Cava Packager is currently distributed under a free to use license.

Supported Perl Versions

Threaded Perl with a shared libperl 5.8, 5.10, 5.12, 5.14, 5.16

Supported Operating Systems

    MS Windows XP and later 32 and 64 bit.

    Linux 32 and 64 bit - minimum glibc 2.5, GTK+ 2.10, libstdc++6.

    Linux 32 bit RHEL 3 and 4.

    Mac OSX 10.4 and 10.5 - ppc and i386.

    Mac OSX 10.6, 10.7, 10.8 - i386 and x86_64 ( 64 bit for Perl 5.16 only ).

Address of the bookmark: http://www.cavapackager.com/

Clean the FASTA file

Jit — Thu, 03 Oct 2013 14:19:14 -0500

Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.

Guest Faculty Job vacancies in Pondicherry University

Tue, 22 Sep 2015 23:50:16 -0500

Guest Faculty Job vacancies in Pondicherry University
Qualification : M.Phil. / M.Tech. / M.Sc. in Computer Science / Master of Computer Applications with a minimum of 55% of marks. Candidates with Ph.D. degree and NET/SLET qualification will be given preference as per UGC norms.

Desirable : Research or teaching experience in Bioinformatics and Computational Biology.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of 25,000/- per month)
How to apply

Interested eligible candidates may attend the 'walk-in' interview along with all original certificates and testimonials with a copy of their bio-data. Walk-in-interview will be held on 28.09.2015 (Monday), 03:00 P.M. at the office of the Dean, School of Life Sciences, Science Block — I, Pondicherry University, Puducherry — 605 014. Candidates reporting after 03:00 P.M. will not be entertained.

More at http://www.pondiuni.edu.in/news/walk-interview-guest-faculty-centre-bioinformatics

Circleator

Jit — Sun, 25 Jun 2017 18:04:32 -0500

The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Common uses of the tool include:

Displaying the sequence and/or genes in a GenBank flat file.
Highlighting differences and/or similarities in gene content between related organisms.
Comparing SNPs and indels between closely-related strains or serovars.
Comparing gene expression values across multiple samples or timepoints.
Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

Builds on BioPerl and the input file formats that it supports, including:
- GenBank flat files, GFF, FASTA
Accepts a number of other commonly-used datatypes and file formats:
- BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
Requires only a single configuration file whose layout mirrors that of the figure itself.
- Predefined configuration files and "track" types are supplied for common datasets.
- Advanced features allow limited analyses to be performed as a figure is drawn.
Includes an extensive set of regression tests.
Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

mojolicious: a next generation web framework for the Perl programming language.

Jit — Fri, 12 Jan 2018 16:48:10 -0600

Back in the early days of the web, many people learned Perl because of a wonderful Perl library called CGI. It was simple enough to get started without knowing much about the language and powerful enough to keep you going, learning by doing was much fun. While most of the techniques used are outdated now, the idea behind it is not. Mojolicious is a new endeavor to implement this idea using bleeding edge technologies.

Features

An amazing real-time web framework, allowing you to easily grow single file prototypes into well-structured MVC web applications.
- Powerful out of the box with RESTful routes, plugins, commands, Perl-ish templates, content negotiation, session management, form validation, testing framework, static file server, CGI/PSGI detection, first class Unicode support and much more for you to discover.
A powerful web development toolkit, that you can use for all kinds of applications, independently of the web framework.
- Full stack HTTP and WebSocket client/server implementation with IPv6, TLS, SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support.
- Built-in non-blocking I/O web server, supporting multiple event loops as well as optional pre-forking and hot deployment, perfect for building highly scalable web services.
- JSON and HTML/XML parser with CSS selector support.
Very clean, portable and object-oriented pure-Perl API with no hidden magic and no requirements besides Perl 5.24.0 (versions as old as 5.10.1 can be used too, but may require additional CPAN modules to be installed)
Fresh code based upon years of experience developing Catalyst, free and open source.
Hundreds of 3rd party extensions and high quality spin-off projects like the Minion job queue.

http://mojolicious.org/

Address of the bookmark: http://mojolicious.org/