BOL: Related items

FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies

Jit — Sat, 01 Jun 2019 03:11:16 -0500

FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results.
The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic areas identified by lead SNPs.
The GENE2FUNC function takes a list of gene IDs (as identified by SNP2GENE or as provided manually) and annotates genes in biological context

Address of the bookmark: https://fuma.ctglab.nl/

ALPHA: A Toolkit for Automated Local Phylogenomic Analyses

Jit — Wed, 21 Mar 2018 18:12:06 -0500

Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic analysis: RAxML, File Converter, MS Comparison, and D-statistic.

Address of the bookmark: https://github.com/chilleo/ALPHA

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Jit — Tue, 12 Jun 2018 12:41:10 -0500

Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs).

Address of the bookmark: https://github.com/ruping/Breakpointer

chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes

BioStar — Sat, 22 Aug 2020 05:17:18 -0500

To create a fresh environment for chromatiblock to run in do:

conda create --name chromatiblock
conda activate chromatiblock
conda install chromatiblock --channel conda-forge --channel bioconda

Then in future to run chromatiblock you can reactivate this environemtn using conda activate chromatiblock

Direct download:

Alternatively you can download and run the script from here.

Address of the bookmark: https://github.com/mjsull/chromatiblock

JBrowse 2: a modular genome browser with views of synteny and structural variation

Abhi — Tue, 25 Apr 2023 20:58:52 -0500

igvjs - a create-react-app with igv package from npm installed. the igv.js is instrumented to output "DONE" to the console when finished, and to have an increased fetchSizeLimit (which is otherwise git in CRAM longread tests)
jb2-web - stock instance of jbrowse-web v1.7.5
jb1 - stock instance of jbrowse 1 v1.16.11
jb2 embedded - a create-react-app with @jbrowse/react-linear-genome-view

Address of the bookmark: https://github.com/GMOD/jb2profile

BRaVa Browser

Jitendra Narayan — Sun, 23 Aug 2026 10:32:19 -0500

BRaVa Browser is an interactive web tool for exploring rare genetic variant associations. It allows users to search and visualize rare variant association results across genes and traits, making it easier to investigate potential relationships between genetic variation and disease or other phenotypes.

More at https://nikbaya.github.io/brava_browser/#/

Address of the bookmark: https://nikbaya.github.io/brava_browser/#/

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants

BioJoker — Tue, 09 Apr 2019 07:23:37 -0500

Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs.

https://www.nature.com/articles/nm.3975

Address of the bookmark: https://www.nature.com/articles/nm.3975

ONT assembly and Illumina polishing pipeline

Jit — Thu, 23 Nov 2017 10:13:42 -0600

This pipeline performs the following steps:

Assembly of nanopore reads using Canu.
Polish canu contigs using racon (optional).
Map a paired-end Illumina dataset onto the contigs obtained in the previous steps using BWA mem.
Perform correction of contigs using pilon and the Illumina dataset.

Address of the bookmark: https://github.com/nanoporetech/ont-assembly-polish

dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements

Rahul Nayak — Sat, 02 Dec 2017 18:25:44 -0600

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).

dnaPipeTE is developped by Clément Goubert, Laurent Modolo and the TREEP team of the LBBE: http://lbbe.univ-lyon1.fr/-Equipe-Elements-transposables-.html?lang=en
You can find the original publication in GBE here: https://academic.oup.com/gbe/article/7/4/1192/533768

output examples of quantification and TE landscape (relative age) produced by dnaPipeTE

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

Ra assembler - a de novo DNA assembler for third generation sequencing data

biogeek — Wed, 27 Dec 2017 20:36:54 -0600

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS).

Ra is in development since 2014 in the form of several separate components that used to be run individually.
This project aims to ease the usage of Ra by integrating it into a complete de novo assembly tool.

Unlike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", https://github.com/isovic/graphmap) and constructing and reducing an overlap graph (Ra layout, https://github.com/mariokostelac/ra).

Address of the bookmark: https://github.com/mariokostelac/ra-integrate/