BOL: Related items

PhyloGrapher - Graph Visualization Tool

Jit — Wed, 07 Mar 2018 18:11:25 -0600

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.

https://www.youtube.com/watch?v=WgufqYMHCvM

Address of the bookmark: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Jit — Wed, 14 Nov 2018 04:50:27 -0600

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

Address of the bookmark: https://github.com/voutcn/megahit

GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.

Jit — Fri, 05 Feb 2021 21:22:24 -0600

GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data. As GraphUnzip only connects sequences in the assembly graph that already had a potential link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and on two real datasets for the genomes of the rotifer Adineta vaga and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies.

https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779.full.pdf

Address of the bookmark: https://github.com/nadegeguiglielmoni/GraphUnzip

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Neel — Fri, 20 May 2016 18:53:49 -0500

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090581

Cancer Dependency Map

Jit — Thu, 13 Feb 2020 04:38:47 -0600

The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This knowledge is foundational for precision cancer medicine.

Address of the bookmark: https://depmap.sanger.ac.uk/

Panacus : A Counting Tool for Pangenome Graphs

Neel — Fri, 14 Jun 2024 14:42:28 -0500

panacus is a tool for calculating statistics for GFA files. It supports GFA files with P and W lines, but requires that the graph is blunt, i.e., nodes do not overlap and consequently, each link (L) points from the end of one segment (S) to the start of another.

panacus supports the following calculations:

coverage histogram
pangenome growth statistics
path-/group-resolved coverage table

Address of the bookmark: https://github.com/marschall-lab/panacus

Mom Knows Best

Jitendra Narayan — Thu, 22 Aug 2013 13:30:43 -0500

We always get instructions to wash our hands, sterilize kitchen stuff and bla bla. However, recent findings suggest something else. Perhaps we can't survive, or will face lots of problems if bacteria’s colonies are absent in mother womb. Please find the detail sources of microbial transmission in humans from mother to child in recently published PLOS paper.

http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001631

Greengenes database

Jit — Wed, 29 Jun 2016 10:03:31 -0500

The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. If you are an ARB user, you can use greengenes to keep your own local database current.

Address of the bookmark: http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure

Rahul Nayak — Sat, 07 Mar 2020 05:52:20 -0600

GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where presence-absence status of acquired genes is usually confounded by bacterial population structure due to clonal reproduction.

https://www.biorxiv.org/content/10.1101/2020.02.29.970970v1

Address of the bookmark: https://github.com/wanyuac/GeneMates

HiBC: Human Intestinal Bacteria Collection

BioStar — Wed, 07 May 2025 05:49:19 -0500

The human gut is home to trillions of microorganisms, forming one of the most complex and dynamic microbial ecosystems known to science. The Human Intestinal Bacteria Collection (HiBC) is a pioneering initiative aimed at cataloging, preserving, and studying the diverse bacterial species that inhabit the human gastrointestinal tract. This curated collection serves as a critical resource for researchers working on microbiome-related health, disease, and therapeutics.

What is HiBC?

The Human Intestinal Bacteria Collection (HiBC) is a comprehensive, high-quality reference repository of bacterial isolates derived from human fecal samples. It focuses on anaerobic and facultative anaerobic bacteria that play pivotal roles in digestion, immune modulation, vitamin synthesis, and pathogen resistance. The collection includes both culturable strains and genomic data from unculturable taxa, bridging the gap between culture-dependent and -independent microbiome studies.

Why is HiBC Important?

Understanding Microbiome-Host Interactions
HiBC enables deeper insight into the functions of specific bacterial taxa in the gut. With well-characterized isolates, researchers can conduct mechanistic studies to explore how certain bacteria influence metabolism, inflammation, or mental health.
Precision Probiotics and Therapeutics
By providing access to native human gut microbes, HiBC supports the development of next-generation probiotics, live biotherapeutic products (LBPs), and fecal microbiota transplantation (FMT) alternatives.
Standardization and Reproducibility
With standardized cultivation and genomic protocols, HiBC ensures consistency across microbiome research studies, improving reproducibility and comparability of findings.
Antimicrobial Resistance (AMR) Surveillance
HiBC includes metadata on antibiotic resistance genes (ARGs), helping track the spread of AMR in commensal gut bacteria and understanding its implications for human health.

Key Features of HiBC

Culturable Bacteria Repository: A living collection of anaerobic and facultative strains isolated from healthy and diseased individuals worldwide.
Metadata-rich Entries: Each isolate is annotated with host details (age, health status, diet), geographical origin, phenotypic traits, and antibiotic susceptibility profiles.
Whole Genome Sequencing (WGS): High-quality genome assemblies for most strains to support functional and comparative genomics.
Interactive Database Access: User-friendly search and filtering options for strain selection based on taxonomy, function, or clinical relevance.
Cross-linking with Other Databases: Integration with NCBI, GOLD, and Human Microbiome Project (HMP) data for broader context and validation.

Applications of HiBC

Microbiome-based diagnostics and biomarker discovery
Host-microbe interaction studies in gnotobiotic mouse models
Gut microbiome modulation through diet, drugs, or engineered bacteria
Longitudinal studies of gut flora across age, geography, and lifestyle
Environmental and evolutionary microbiology of human-associated bacteria

Accessing HiBC

Researchers and interested parties can explore the HiBC database through its official website: https://www.hibc.rwth-aachen.de/. The platform offers comprehensive information on bacterial isolates, including taxonomy, cultivation conditions, and genomic data, facilitating advanced research in human gut microbiome studies.

Final Thoughts

The HiBC is a cornerstone resource in the rapidly evolving field of microbiome research. As science moves toward personalized medicine and microbial therapeutics, having a reliable and diverse collection of human gut bacteria is not just useful — it's essential. Whether you're a microbiologist, clinician, computational biologist, or biotechnologist, HiBC offers tools to accelerate discovery and innovation in gut microbiome science.