BOL: Related items

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

TULIP - The Uncorrected Long read Itegration Pipeline

Jit — Thu, 23 Nov 2017 09:30:01 -0600

#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel)

TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow.
Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.

https://github.com/Generade-nl/TULIP

Address of the bookmark: https://github.com/Generade-nl/TULIP

PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens

LEGE — Wed, 21 Feb 2024 06:15:13 -0600

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

Address of the bookmark: https://github.com/lmcai/PhyloHerb/

Webinar on Streamlining large scale analysis using the Strand NGS Pipeline Manager on 24 Feb 2016

Yeshodari — Fri, 05 Feb 2016 06:43:28 -0600

Live Webinar on Streamlining large scale NGS data analysis using the Strand NGS Pipeline Manager on 24 Feb 2016

Abstract: Strand NGS includes comprehensive workflows for DNA-Seq, RNA-Seq, Small RNA-Seq, ChIP-Seq, MeDIP-Seq, and Methyl-Seq analysis. Each workflow includes a quality assessment and filter section, followed by a workflow-specific analysis section. The pipeline functionality in Strand NGS allows users to execute a sequence of analysis steps with specific parameters - all without any manual intervention. This simplifies the analysis in large scale sequencing projects where every sample needs to be processed identically.

In this webinar we will discuss the pre-packaged pipelines present in Strand NGS. The packaged pipelines have well-chosen default parameters and are suitable for users analyzing data for the first time in the tool. We will also show how advanced users can customize pipelines and share them with other Strand NGS users. Finally, we will show a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and emails quality reports - all from within Strand NGS.

Speaker: Dr. Vamsi Veeramachaneni, Vice President - Bioinformatics, Strand Life Sciences

Details: Session 1: 2:30 PM IST, Session 2 : 10:30 PM IST
Register here: http://www.strand-ngs.com/webinar_registration

ARC: pipeline which facilitates iterative, reference guided de novo assemblies

Jit — Thu, 26 Jul 2018 09:20:26 -0500

ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of:

Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble together.
Reducing/removing reference bias as compared to mapping based approaches.

The software is designed to work in situations where a whole-genome assembly is not the objective, but rather when the researcher wishes to assemble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into small, manageable subsets which can then be assembled quickly and efficiently in parallel. Applications include those in which the researcher wishes to de novo assemble specific content and a set of semi-similar reference targets is available to initialize the assembly process.

https://ibest.github.io/ARC/

Address of the bookmark: https://ibest.github.io/ARC/

dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements

Jit — Mon, 12 Aug 2019 21:56:08 -0500

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

https://github.com/clemgoub/dnaPipeTE/wiki/dnaPipeTE-WIKI-home

Address of the bookmark: https://github.com/clemgoub/dnaPipeTE

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Thu, 14 May 2020 15:13:30 -0500

gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/

Address of the bookmark: https://github.com/kammoji/gapFinisher

SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins

BioStar — Mon, 17 Aug 2020 05:25:10 -0500

SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:

Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome
Co-assembly of a large number of metagenomes via merging of individual metagenomes
Includes binning and bin checking, for retrieving individual genomes
The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.
Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.
Metatranscriptomic support via mapping of cDNA reads against reference metagenomes

Address of the bookmark: https://github.com/jtamames/SqueezeMeta

List of universities offering Bachelor, Master or PhD bioinformatics degree in Malaysia

sahabuddin — Thu, 22 Jun 2017 01:34:02 -0500

Bioinformatics is a newly emerging interdisciplinary research area, which may be defined as the ―interface between biological and computational sciences. Most of the Bioinformatics work that is done can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. The global Bioinformatics industry has grown at a double-digit growth rate in the past and is expected to follow the same pattern in the next four years. US remains the largest market in the world, but Asia-Pacific countries, particularly India and China, are witnessing the fastest growth and are anticipated to emerge as the dominating forces in future. The Comparison of Bioinformatics Industry between Malaysia, India and other countries are discussed in this http://ijbssnet.com/journals/Vol.%202_No._10;_June_2011/11.pdf paper.

Bioinformatics is full of opportunities. The sector is poised to open new avenues for the other related sectors also. But the biggest opportunity area in the Bioinformatics market will be in the drug discovery sector. Reduction of both the cost and time taken to discover a new drug due to fast development in the Bioinformatics tools and software zone is also making drug discovery an attractive field to venture in. Malaysian bioinformatics growth and future are discuss in this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper. Keeping all such inportance in mind, following universities in Malaysia offering bioinformatics cources:

3 program(s) at AIMST University, Malaysia

Master of Science in Biotechnology (MSc) - Bioinformatics by Research

Master of Science (M.Sc) in Medical Microbiology (Bioinformatics) by Research

Doctor of Philosophy in Biotechnology (PhD) - Bioinformatics by Research

1 program(s) at INTI International University and Colleges, Malaysia

American Degree Transfer Program (Biosciences) in Bioinformatics

3 program(s) at Management and Science University (MSU), Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

1 program(s) at Multimedia University (MMU), Malaysia

Bachelor of Science (Honours) Bioinformatics

1 program(s) at Universiti Industri Selangor (UNISEL) Bestari Jaya Campus, Malaysia

Bachelor of Bioinformatics (Hons)

2 program(s) at Universiti Malaysia Sabah (UMS), Malaysia

PhD - Doctor of Philosophy in Bioinformatics (By Research)

MSc - Master of Science in Bioinformatics (By Research)

6 program(s) at Universiti Putra Malaysia (UPM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master of Science in Bioinformatics and System Biology by Research

Master of Science (M.Sc) in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics by Research

PhD - Doctor of Philosophy in Bioinformatics and Systems Biology (With Thesis)

PhD - Doctor of Philosophy in Bioinformatics and System Biology by Research

1 program(s) at Universiti Selangor (UNISEL), Malaysia

Bachelor of Bioinformatics (Hons)

3 program(s) at Universiti Teknologi Malaysia (UTM), Malaysia

M.Sc - Master of Science (Bioscience) in Bioinformatics Research Group (BIRG) By Research

PhD - Doctor of Philosophy (Bioscience) in Bioinformatics Research Group (BIRG) By Research

Bachelor of Computer Science (BioInformatics)

4 program(s) at University of Malaya (UM), Malaysia

MSc - Master of Science in Bioinformatics by Research

Master in Bioinformatics by Coursework

PhD - Doctor of Philosophy in Bioinformatics by Research

Bachelor of Science (BSc) in Bioinformatics

3 program(s) at Perdana University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

3 program(s) at Monash University, Malaysia

Master in Bioinformatics (By Research)

PhD in Bioinformatics

Bachelor in Bioinformatics (Hons)

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue. For detail Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges are discussed in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723929/ paper.

LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

LEGE — Fri, 17 Sep 2021 01:57:02 -0500

The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed lncRNAs annotation strategy, optimized calculating efficiency, diversified classification and interactive analysis report. LncPipe allows users additional control in interuppting the pipeline, resetting parameters from command line, modifying main script directly and resume analysis from previous checkpoint.

Ref https://www.lncrnablog.com/lncpipe-a-nextflow-based-pipeline-for-identification-and-analysis-of-long-non-coding-rnas-from-rna-seq-data/

Address of the bookmark: https://github.com/likelet/LncPipe