BOL: Related items

Next generation sequencing(NGS) books

Abhimanyu Singh — Fri, 30 May 2014 04:48:04 -0500

Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

DIAL

Abhimanyu Singh — Wed, 01 Mar 2017 08:42:28 -0600

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management.

http://www.bx.psu.edu/~ratan/

Address of the bookmark: http://www.bx.psu.edu/miller_lab/

Roary: the Pan Genome Pipeline

Jit — Tue, 22 Jan 2019 05:52:07 -0600

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM. Roary is not intended for meta-genomics or for comparing extremely diverse sets of genomes.

Address of the bookmark: https://sanger-pathogens.github.io/Roary/

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Abhi — Wed, 15 May 2024 14:36:12 -0500

Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

Bioinformatician in pipeline development

Tue, 17 Dec 2024 23:43:54 -0600

Are you interested in working with pipeline development in bioinformatics, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a position as Bioinformatician in pipeline development at Uppsala University.

National Bioinformatics Infrastructure Sweden (NBIS) (nbis.se) plays an important role in advancing life science research in Sweden by providing expert support and developing cutting-edge bioinformatics infrastructure. Operating as a truly national initiative, NBIS employs more than 120 bioinformaticians, system developers, and data stewards across multiple locations in Sweden. It serves as the bioinformatics platform at SciLifeLab, a national resource that facilitates research in molecular biosciences by offering access to state-of-the-art technologies and technical expertise. With strong ties to data-producing facilities and ongoing collaborations with leading research groups, NBIS is ideally positioned to support world-class bioinformatics analyses. Furthermore, NBIS is the Swedish node in ELIXIR, the European infrastructure for biological information.

NBIS is seeking an experienced bioinformatician to support both Swedish and international projects. As part of our dynamic team, you will work closely with researchers to process large-scale biological data and contribute to advancing our data analysis infrastructure. Strong problem-solving skills, attention to detail, and the ability to troubleshoot complex bioinformatics pipelines are essential for success in this role. Flexibility and a willingness to learn are also important, as NBIS continually adapts to meet the evolving needs of the Swedish research community.

More at https://www.uu.se/en/about-uu/join-us/jobs-and-vacancies/job-details?query=778701

Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence

Jit — Thu, 23 Nov 2017 08:37:15 -0600

Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).

Address of the bookmark: https://sourceforge.net/projects/taxoblast/files/

PGAP-X: Extension on pan-genome analysis pipeline

Rahul Nayak — Tue, 23 Jan 2018 11:41:43 -0600

PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Serials of algorithms and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene distribution with different conservative levels, and genetic variation from pan-genome sight. At the same time, analytical result data from many other programs, including genome alignment result and orthologs clusters, are also supported to be further analyzed or visualized in PGAP-X. The workflow and feature snapshot in PGAP-X were shown as Fig.1 and Fig.2.

Address of the bookmark: https://pgapx.ybzhao.com/

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

Jit — Tue, 22 Jan 2019 06:26:55 -0600

Run a pipeline processing fast5s to a consensus in a single command.
Recommended fixed "standard" and "fast" pipelines.
Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
Seemless distribution of tasks over local or distributed compute.
Highly configurable.
Open source (Mozilla Public License 2.0).

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

HaploTypo: a variant-calling pipeline for phased genomes

Jit — Thu, 19 Dec 2019 07:33:40 -0600

An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome.

Availability and Implementation

HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image.

Address of the bookmark: https://github.com/gabaldonlab/haplotypo

SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.

Jit — Fri, 14 Feb 2020 14:23:30 -0600

This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.

Here is an illustration of this pipeline:

Address of the bookmark: https://github.com/BGI-Qingdao/SLR-superscaffolder