BOL: Related items

Lorikeet: Strain resolver for metagenomics

BioStar — Sat, 06 Jul 2024 04:21:31 -0500

Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially active regions within candidate genomes. Called variants can be clustered into likely strains using a combination of UMAP and HDBSCAN.

Address of the bookmark: https://github.com/rhysnewell/Lorikeet

MetaSim A Sequencing Simulator for Genomics and Metagenomics.

Jit — Mon, 04 Dec 2017 07:18:20 -0600

Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree.

Address of the bookmark: http://ab.inf.uni-tuebingen.de/software/metasim/

From DNA Chaos to a Clear Microbial Story

BioStar — Fri, 21 Aug 2026 11:22:54 -0500

Imagine opening a metagenomic dataset and finding millions of DNA fragments, each carrying a tiny piece of information about the microbial world inside a sample. The challenge is not generating the data — it is turning that data into a meaningful story.

This is where MeTAline comes in.

MeTAline is a reproducible workflow designed to simplify shotgun metagenomic analysis. It brings together important steps such as quality control, host-DNA removal, taxonomic profiling and functional analysis, using tools including Kraken2, MetaPhlAn4 and HUMAnN.

What makes it especially useful is its ability to handle large datasets while keeping analyses organized and reproducible. Built with Snakemake and supporting containerized environments, MeTAline can also be used on high-performance computing systems.

In simple terms, MeTAline helps researchers move from millions of confusing DNA fragments to a clearer picture of who is there, what they might be doing, and what the data could mean.

Sometimes, the biggest challenge in science isn't collecting more data — it's finding the story hidden inside it.

Read more at https://academic.oup.com/nargab/article/7/4/lqaf158/8340158?login=false

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/

SWALO: Scaffolding with assembly likelihood optimization

Jit — Wed, 20 Jun 2018 02:45:16 -0500

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.

Address of the bookmark: https://atifrahman.github.io/SWALO/

wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly

BioStar — Mon, 04 Feb 2019 04:53:47 -0600

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.

./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix
./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa

Address of the bookmark: https://github.com/ruanjue/wtdbg2

TRITEX sequence assembly pipeline for Triticeae genomes

Jit — Tue, 20 Aug 2019 09:47:14 -0500

The pipeline is open-source and hosted in a public Bitbucket repository.

TRITEX has been run on highly inbred genotypes of barley (Hordeum vulgare), tetraploid wheat (Triticum turgidum) and hexaploid wheat (T. aestivum) with reasonable results: super-scaffold N50 values in the range of dozens of Mb and pseudomolecules with better gene space representation than a BAC-by-BAC assembly. It has never been tested and is not expected to work on heterozygous or autopolyploid genomes.

A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelbach et al. 2018. Refer to the technical notes of 10X Genomics on how to generate Chromium data.

Address of the bookmark: https://tritexassembly.bitbucket.io/

Free Genomics data !

BioStar — Fri, 07 Feb 2020 14:08:31 -0600

The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/