BOL: Related items

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

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

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

3D de novo assembly (3D DNA) pipeline

Jit — Sun, 02 Feb 2020 13:41:55 -0600

For a detailed description of the pipeline and how it integrates with other tools designed by the Aiden Lab see Genome Assembly Cookbook on http://aidenlab.org/assembly.

For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in (Dudchenko et al., Science, 2017) see the original commit.

For the detailed description of the merge section see https://github.com/theaidenlab/AGWG-merge.

Address of the bookmark: https://github.com/theaidenlab/3d-dna

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

LEGE — Thu, 23 Jul 2020 05:52:56 -0500

WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2670-3

Address of the bookmark: https://github.com/yongzhiyang2012/wgddetector

CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes

Jit — Wed, 10 Mar 2021 06:13:49 -0600

The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in improved contig N50 when compared to current state of the art methods.

For smaller vertebrate genomes (~1 Gbp) chromosome scale assemblies can be achieved within 12h on high-end Desktop computers (Intel i7, 12 CPU threads, 128 GB RAM). Larger mammalian genomes (~3Gbp) can be processed within 15-18 h on server equipment (Xeon, 96 CPU threads, 1TB RAM).

Address of the bookmark: https://github.com/HMPNK/CSA2.6

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

pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction

LEGE — Wed, 21 Feb 2024 06:19:41 -0600

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake