BOL: Related items

MITObim - mitochondrial baiting and iterative mapping

Rahul Nayak — Tue, 08 May 2018 04:15:25 -0500

This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed for Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms.

Below you can find a few basic tutorials for how to run MITObim and I encorage you to give them a try with the testdata that comes with this Repo, just to make sure everything is running smoothly on your system. It'll only take a few minutes and will potentially safe you a lot of time down the line.

I provide further examples here as Jupyter notebooks. Get in touch if you feel like sharing your particular MITObim solution and I'd be happy to put it up here, too!

Address of the bookmark: https://github.com/chrishah/MITObim

vcfR: a package to manipulate and visualize VCF data in R

Jit — Thu, 25 Oct 2018 09:05:59 -0500

VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.

Address of the bookmark: https://github.com/knausb/vcfR

Tools for RNA classification

Abhi — Tue, 08 Nov 2022 03:39:11 -0600

barrnap - https://github.com/tseemann/barrnap

CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

Bioinformatics Tools for Phylogeny !

BioStar — Mon, 06 Nov 2023 03:09:59 -0600

Direct access to the individual tools available on this server.

Multiple Alignment:	Phylogeny:	Tree viewers:	Utilities:
MUSCLE	PhyML	TreeDyn	Gblocks
T-Coffee / 3DCoffee	TNT	Drawgram	Jalview
ClustalW	BioNJ	Drawtree	Readseq
ProbCons	MrBayes	ATV (A Tree Viewer)	Built-in converter

Mycology Research Resources for Bioinformaticians: Unlocking the Fungal Kingdom

Neel — Fri, 13 Dec 2024 11:21:45 -0600

Mycology, the study of fungi, is a field that bridges ecology, medicine, and biotechnology. With advancements in bioinformatics, researchers now have unprecedented opportunities to explore the fungal kingdom at molecular, genetic, and ecological levels. From understanding pathogenic fungi to harnessing fungal enzymes for industrial applications, the potential is vast.

To fully leverage these opportunities, bioinformaticians require specialized tools and databases. This blog highlights essential resources for mycology research, focusing on databases, tools, and platforms tailored for fungal biology.

1. Fungal Databases

1.1. MycoCosm

Website: MycoCosm
Developed by the DOE Joint Genome Institute, MycoCosm is a comprehensive portal for fungal genomics. It offers genomic and transcriptomic data for a wide range of fungi, including saprobes, pathogens, and symbionts.

Key Features: Genome browsers, comparative genomics tools, and functional annotations.
Best For: Large-scale studies on fungal evolution and ecology.

1.2. FungiDB

Website: FungiDB
FungiDB is an integrated genomic resource for fungal pathogens and non-pathogens. It provides access to genome sequences, transcriptomic data, and functional annotations.

Key Features: Advanced search options, BLAST, and pathway analysis tools.
Best For: Studying fungal pathogenesis and host-pathogen interactions.

1.3. Index Fungorum

Website: Index Fungorum
This nomenclatural database provides information on the scientific names of fungi. It’s an essential resource for taxonomists and researchers focused on fungal biodiversity.

Key Features: Taxonomic hierarchy and synonymy tracking.
Best For: Identifying and classifying fungal species.

1.4. UNITE

Website: UNITE
UNITE is a specialized database for fungal ITS (Internal Transcribed Spacer) sequences, often used in fungal identification and phylogenetics.

Key Features: Curated reference datasets and community annotations.
Best For: Environmental mycology and microbial ecology studies.

2. Analytical Tools

2.1. Funannotate

Repository: GitHub - Funannotate
Funannotate is a genome annotation tool designed for fungi. It supports tasks like gene prediction, functional annotation, and orthology analysis.

Best For: Annotating newly sequenced fungal genomes.

2.2. BUSCO (Benchmarking Universal Single-Copy Orthologs)

Website: BUSCO
BUSCO evaluates genome assembly and annotation completeness using orthologs. It includes a fungal-specific dataset.

Best For: Assessing the quality of fungal genome assemblies.

2.3. Pathogen-Host Interactions Database (PHI-base)

Website: PHI-base
PHI-base is a manually curated resource containing information on pathogen-host interactions, including fungal pathogens.

Best For: Exploring virulence factors and host-pathogen relationships.

3. Visualization Platforms

3.1. Cytoscape

Website: Cytoscape
A powerful tool for visualizing molecular interaction networks, Cytoscape can be used to study protein-protein interactions, gene networks, and metabolic pathways in fungi.

Best For: Network biology and functional genomics.

3.2. iTOL (Interactive Tree of Life)

Website: iTOL
iTOL is an interactive tool for visualizing phylogenetic trees.

Best For: Displaying fungal phylogenies and comparing evolutionary relationships.

4. Community Resources

4.1. Mycological Society of America (MSA)

Website: MSA
The MSA promotes fungal research and provides access to resources, conferences, and publications.

Best For: Networking with fungal researchers and accessing recent studies.

4.2. OpenFungi

Website: OpenFungi
OpenFungi is an open-source initiative providing fungal genomic and transcriptomic datasets for research and education.

Best For: Sharing and accessing public fungal datasets.

5. Genomics Workflows

5.1. Galaxy

Website: Galaxy Project
Galaxy offers a web-based platform for reproducible bioinformatics workflows, including tools for fungal genome and transcriptome analysis.

Best For: User-friendly analysis pipelines without requiring coding skills.

5.2. Snakemake

Repository: Snakemake
A flexible pipeline management tool that supports fungal data processing and analysis.

Best For: Custom workflows for large-scale fungal datasets.

Conclusion

Fungal research is a rapidly growing field with vast implications for medicine, agriculture, and industry. For bioinformaticians, the availability of specialized resources—databases, tools, and community platforms—opens doors to innovative discoveries. Whether you are investigating fungal genomics, studying host-pathogen interactions, or exploring fungal biodiversity, the resources outlined above will empower your research journey.

Dive into these resources and help unravel the mysteries of the fungal kingdom!

Alignment-free sequence comparison tools available for next-generation sequencing data analysis

Abhimanyu Singh — Tue, 07 Nov 2017 05:33:33 -0600

kallisto

Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)

Software (C++)

https://pachterlab.github.io/kallisto/

Sailfish

Estimation of isoform abundances from reference sequences and RNA-seq data (k-mer based)

Software (C++)

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Salmon

Quantification of the expression of transcripts using RNA-seq data (uses k-mers)

https://combine-lab.github.io/salmon/

RNA-Skim

RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses sig-mers, a special type of k-mers)

Software (C++)

http://www.csbio.unc.edu/rs/

Variant calling

ChimeRScope

Fusion transcript prediction using gene k-mers profiles of the RNA-seq paired-end reads

Software (Java)

https://github.com/ChimeRScope/ChimeRScope/wiki

FastGT

Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique k-mers

Software (C)

https://github.com/bioinfo-ut/GenomeTester4/

Phy-Mer

Reference-independent mitochondrial haplogroup classifier from NGS data (k-mer based)

Software (Python)

https://github.com/danielnavarrogomez/phy-mer

LAVA

Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (k-mer based)

Software (C)

http://lava.csail.mit.edu/

MICADo

Detection of mutations in targeted third-generation NGS data (can distinguish patients’ specific mutations; algorithm uses k-mers and is based on colored de Bruijn graphs)

Software (Python)

http://github.com/cbib/MICADo

General mapper

Minimap

Lightweight and fast read mapper and read overlap detector (uses the concept of “minimazers”, a special type of k-mers)

Software (C)

https://github.com/lh3/minimap

Assembly

De novo genome assembly

MHAP

Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash

Software (Java)

https://github.com/marbl/MHAP

Miniasm

Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)

Software (C)

https://github.com/lh3/miniasm

LINKS

Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)

Software (Perl)

https://github.com/warrenlr/LINKS/

Read clustering

afcluster

Clustering of reads from different genes and different species based on k-mer counts

Software (C++)

https://github.com/luscinius/afcluster

QCluster

Clustering of reads with alignment-free measures (k-mer based) and quality values

Software (C++)

http://www.dei.unipd.it/~ciompin/main/qcluster.html

Reads error correction

Lighter

Correction of sequencing errors in raw, whole genome sequencing reads (k-mer based)

Software (C++)

https://github.com/mourisl/Lighter

QuorUM

Error corrector for Illumina reads using k-mers

Software (C++)

https://github.com/gmarcais/Quorum

Trowel

Software (C++)

https://sourceforge.net/projects/trowel-ec/

Metagenomics

Assembly-free phylogenomics

AAF

Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (k-mer based)

Software (Python)

https://github.com/fanhuan/AAF

kSNP v3

Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on k-mer analysis)

Software (C)

https://sourceforge.net/projects/ksnp/files/

NGS-MC

Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2 S under different Markov chain models (using k-words)

R package

http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html

Species identification/taxonomic profiling

CLARK

Taxonomic classification of metagenomic reads to known bacterial genomes using k-mer search and LCA assignment

Software (C++)

http://clark.cs.ucr.edu/

FOCUS

Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)

Web service Software (Python)

http://edwards.sdsu.edu/FOCUS/

GSM

Estimation of abundances of microbial genomes in metagenomic samples (k-mer based)

Software (Go)

https://github.com/pdtrang/GSM

Mash

Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)

Software (C++)

https://github.com/marbl/mash

Kraken

Taxonomic assignment in metagenome analysis by exact k-mer search; LCA assignment of short reads based on a comprehensive sequence database

Software (C++)

https://ccb.jhu.edu/software/kraken/

LMAT

Assignment of taxonomic labels to reads by k-mers searches in precomputed database

Software (C++/Python)

https://sourceforge.net/projects/lmat/

stringMLST

k-mer-based tool for MLST directly from the genome sequencing reads

Software (Python)

http://jordan.biology.gatech.edu/page/software/stringMLST

Taxonomer

k-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples

Web service

http://taxonomer.iobio.io/

Other

d2-tools

Word-based (k-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads

Software (Python/R)

https://code.google.com/p/d2-tools/

VirHostMatcher

Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)

Software (C++)

https://github.com/jessieren/VirHostMatcher

MetaFast

Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissimilarity measure

Software (Java)

https://github.com/ctlab/metafast

List of visualization tools for network biology

Jit — Mon, 29 Jan 2018 05:12:24 -0600

Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which makes it possible to infer details about the network as a whole at the species and/or population level. Few tools published in BMC are listed here https://bmcbioinformatics.biomedcentral.com/articles/sections/networks-analysis.

Following are the list of standalone applications for network analysis:

Arena 3D

3D visualization of multi-layer networks

http://www.arena3d.org

Biana

Data integration and network management

http://sbi.imim.es/web/BIANA.php

BioLayout Express 3D

2D/3D network visualization

http://www.biolayout.org/

BiologicalNetworks

Efficient integrated multi-level analysis of microarray, sequence, regulatory and other data

http://www.biologicalnetworks.org

BioMiner

Modeling, analyzing and visualizing biochemical pathways and networks

http://www.zbi.uni-saarland.de/chair/projects/BioMiner

Cell Illustrator

Petri nets for modeling and simulating biological networks

http://www.cellillustrator.com

COPASI

Analysis of biochemical networks and their dynamics

http://www.copasi.org/

Cytoscape

Network visualization and analysis. Over 200 plugins [60]

http://www.cytoscape.org/

Dizzy

Chemical kinetics stochastic simulation software

http://magnet.systemsbiology.net/software/Dizzy/

DyCoNet

Gephi plugin that can be used to identify dynamic communities in networks

https://github.com/juliemkauffman/DyCoNet

GENeVis

Network and pathway visualization

http://tinyurl.com/genevis/

GEPHI

Interactive visualization and exploration for any network and complex system, dynamic and hierarchical graph.

https://gephi.org

Igraph

Collection of network analysis tools with the emphasis on efficiency, portability and ease of use

http://igraph.sourceforge.net

Medusa

Semantic and multi-edged simple networks

https://sites.google.com/site/medusa3visualization/

NAViGaTOR

Visualizing and analyzing protein-protein interaction networks

http://tinyurl.com/navigator1/

N-Browse

Interactive graphical browser for biological networks

http://www.gnetbrowse.org/

NeAT

Topological and clustering analysis of networks

http://rsat.ulb.ac.be/neat/

Ondex

Data integration and visualization of large networks

http://www.ondex.org/

Osprey

Visualization and annotation of biological networks

http://biodata.mshri.on.ca/osprey/servlet/Index

Pajek

Analysis and visualization of large networks and social network analysis

http://vlado.fmf.uni-lj.si/pub/networks/pajek/

PathwayAssist

Navigation and analysis of biological pathways, gene regulation networks and protein interaction maps.

http://www.ariadnegenomics.com/downloads/

PIVOT

Layout algorithms for visualizing protein interactions and families

http://acgt.cs.tau.ac.il/pivot/

ProCope

Prediction and evaluation of protein complexes from purification data experiments

http://www.bio.ifi.lmu.de/Complexes/ProCope/

ProViz

Visualization and exploration of interaction networks. Gene Ontology and PSI-MI formats supported

http://cbi.labri.fr/eng/proviz.htm

SpectralNET

Network analysis and visualizations. Scatter plots and dimensionality reduction algorithms

https://www.broadinstitute.org/software/spectralnet

Tulip

Enables the development of algorithms, visual encodings, interaction techniques, data models and domain-specific visualizations

http://tulip.labri.fr/TulipDrupal/

VANESA

Automatic reconstruction and analysis of biological networks and Petri nets based on life-science database information

http://agbi.techfak.uni-bielefeld.de/vanesa/

VANTED

Network reconstruction, data visualization, integration of various data types, network simulation

http://tinyurl.com/vanted/

yEd

Creation of diagrams manually and import external data

http://tinyurl.com/yEdGraph/

Web tools for network analysis

APID

Unified protein-protein interactions from BIND, BioGRID, DIP, HPRD, IntAct and MINT

http://bioinfow.dep.usal.es/apid/

Arcadia

Translates text-based descriptions of biological networks (SBML files) into standardized diagrams (Systems Biology Graphical Notation Process Description maps)

http://arcadiapathways.sourceforge.net/

AVIS

Viewer for signaling networks

http://actin.pharm.mssm.edu/AVIS2

bioPIXIE

Discovery of biological networks from diverse functional genomic data

http://pixie.princeton.edu/pixie

CellPublisher

Interactive representations of biochemical processes

http://cellpublisher.gobics.de/

Graphle

Distributed network exploration and visualization of interactive large, dense graphs

http://tinyurl.com/graphle/

GraphWeb

Web server for graph-based analysis of biological networks

http://biit.cs.ut.ee/graphweb/

Hubba

Web-based service to explore the essential nodes in a network

http://hub.iis.sinica.edu.tw/Hubba

NetworkBLAST

Analysis of protein interaction networks across species to infer protein complexes that are conserved in evolution

http://www.cs.tau.ac.il/~bnet/networkblast.htm

Pathview

Tool set for pathway-based data integration and visualization

http://Pathview.r-forge.r-project.org/

PINA

Integrated platform for protein interaction network construction, filtering, analysis, visualization and management

http://cbg.garvan.unsw.edu.au/pina/home.do

ReMatch

Web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources

http://www.cs.helsinki.fi/group/sysfys/software/rematch/

SNOW

Gene mapping on a reference or human protein-protein interaction network that SNOW hosts

http://snow.bioinfo.cipf.es

STITCH

Resource to explore known and predicted interactions of chemicals and proteins

http://stitch.embl.de/

STRING

Protein interaction networks and integration of data such as genomic context, high-throughput experiments, conserved coexpression and previous knowledge derived from the literature

http://string-db.org

TVNViewer

An interactive visualization tool for exploring networks that change over time or space

http://www.sailing.cs.cmu.edu/main/?page_id=545

tYNA

System for managing, comparing and mining multiple networks

http://tyna.gersteinlab.org/tyna/

VisANT

Visualization, mining, analysis and modeling of biological networks, metabolic networks and ecosystems

http://visant.bu.edu/

DNA Nucleotide Counter

Neel — Fri, 12 Oct 2018 04:37:01 -0500

DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

Bioinformatics tools for telomere to telomere assembly !

BioStar — Tue, 17 Aug 2021 13:17:09 -0500

● Merfin – k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)
● PanGenie – algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)
● SQANTI3 – an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Rocío Amorín de Hegedüs @rocioadh)
● tama (Transcriptome Annotation by Modular Algorithms) – software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo @GenomeRIK)
● pbaa (PacBio Amplicon Analysis) – separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg @zevkronenberg)
● bellerophon – analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng @Yuanyuan929)
● svpack – tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)
● JumboDB – tool for de Bruijn graph construction (Anton Bankevich @AntonBankevich)
● uLTRA – tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin @krsahlin)
● LeafGo – workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini @ermini_luca)

Reference:

https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/

BioKit: a set of tools dedicated to bioinformatics, data visualisation

Neel — Tue, 18 Jun 2024 02:04:39 -0500

BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis (e.g., biokit.stats). Since R is quite common in bioinformatics, we also provide a convenient module to run R inside your Python scripts or shell (:mod:biokit.rtools module).

Address of the bookmark: https://biokit.readthedocs.io/en/latest/index.html