BOL: Related items

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

Pango Lineage Analysis !

Abhi — Mon, 15 Nov 2021 03:38:29 -0600

The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

SeqCAT: Sequence Conversion and Analysis Toolbox

Neel — Fri, 14 Jun 2024 14:36:53 -0500

Your all-in-one solution for smooth conversion of sequence coordinates.

Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic events such as fusions with SeqCAT.

More at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae422/7683049?login=false

Address of the bookmark: https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/home

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

Jit — Fri, 08 Dec 2017 16:48:40 -0600

Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to Tom Slezak for revsing the get_genbank_file3 script and to Tod Stuber (USDA) for testing version 3.1 even though he doesn't need the annotation feature. All users are encouraged to upgrade to version 3.1.

Address of the bookmark: https://sourceforge.net/projects/ksnp/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/

bpRNA: large-scale automated annotation and analysis of RNA secondary structure

Rahul Nayak — Wed, 23 May 2018 03:24:33 -0500

bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature.

The bpRNA code is written in perl and requires the Graph perl module. Several additional scripts for analysis are included. The source code is available at http://github.com/hendrixlab/bpRNA.

Address of the bookmark: http://github.com/hendrixlab/bpRNA

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

netGO: R-Shiny package for network-integrated pathway enrichment analysis

Jit — Wed, 12 Feb 2020 12:40:54 -0600

netGO is an R/Shiny package for network-integrated pathway enrichment analysis.
netGO provides user-interactive visualization of enrichment analysis results and related networks.

Currently, netGO supports analysis for four species (Human, Mouse, Arabidopsis thaliana,and Yeast)
These data are available from netGO-Data repository.

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa077/5728635

Address of the bookmark: https://github.com/unistbig/netGO

Sample bandage input file for visual analysis

Jit — Wed, 06 Jan 2021 03:51:50 -0600

Sample bandage input file for visual analysis ...