BOL: Related items

Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup

Jit — Sat, 13 Apr 2019 08:55:31 -0500

Darwin-WGA, is the first hardware accelerator for whole genome alignment and accelerates the gapped filtering stage. Darwin-WGA also employs GACT-X, a novel algorithm used in the extension stage to align arbitrarily long genome sequences using a small on-chip memory, that provides better quality alignments at 2× improvement in memory and speed over the previously published GACT algorithm. Implemented on an FPGA, Darwin-WGA provides up to 24× improvement (performance/$) in WGA over iso-sensitive software.

https://stanford.edu/~yatisht/pubs/darwin-wga.pdf

Address of the bookmark: https://github.com/gsneha26/Darwin-WGA

RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs

Jit — Sun, 27 Oct 2019 00:57:23 -0500

Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019.

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
Intact ordering and orienting of contigs.
Misassembly correction
GFF lift-over
Structural variant calling with and integrated version of Assemblytics
Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

U-Plot: Genome U-Plot sample implementation

Rahul Nayak — Tue, 03 Mar 2020 01:39:12 -0600

The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.

Address of the bookmark: https://github.com/gaitat/GenomeUPlot

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Neel — Sun, 20 Dec 2020 01:39:54 -0600

The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short (Illumina) and long (ONT and PacBio) reads. Described by Alser et al. (preliminary version at https://arxiv.org/abs/1910.09020).

Address of the bookmark: https://github.com/CMU-SAFARI/SneakySnake

QuasiModo - Quasispecies Metric Determination on Omics

Neel — Sat, 26 Jun 2021 15:22:56 -0500

This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each consisting of two lab strains in different abundance ratios. This tool can also be used to evaluate assemblies and variant calling results on other similar datasets.

https://academic.oup.com/bib/article/22/3/bbaa123/5868070

Address of the bookmark: https://github.com/hzi-bifo/Quasimodo

OGDRAW - Draw Organelle Genome Maps

Abhi — Tue, 05 Oct 2021 03:34:35 -0500

OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files. The application is optimized to create detailed high-quality maps of organellar genomes (plastid and mitochondria). Nevertheless, you can upload most database entries.

Please take a look at our FAQ section and do not hesitate to report bugs or suggestions for improvements by email.

Address of the bookmark: https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

UniqueKmer: Generate unique KMERs for every contig in a FASTA file

Abhi — Fri, 17 Dec 2021 00:08:15 -0600

Generate unique k-mers for every contig in a FASTA file.

Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).

This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig.

The output unique k-mer file and Genome file can be used for fastv: https://github.com/OpenGene/fastv, which is an ultra-fast tool to identify and visualize microbial sequences from sequencing data.

https://github.com/OpenGene/UniqueKMER

Address of the bookmark: https://github.com/OpenGene/UniqueKMER

Comparative Genomics Workshops !

Rahul Nayak — Tue, 25 Jan 2022 20:39:58 -0600

This meeting's objective was to obtain a big picture look at the current state of the field of comparative genomics with a focus on commonalities across genomic investigations into humans, model organisms (both traditional and non-traditional), agricultural species, wildlife species and microbes.

https://www.genome.gov/event-calendar/perspectives-in-comparative-genomics-and-evolution

Address of the bookmark: https://www.genome.gov/event-calendar/perspectives-in-comparative-genomics-and-evolution

Environmental Genomics Group SciLifeLab/KTH Stockholm

BioStar — Thu, 01 Dec 2022 01:12:43 -0600

Useful Metagenomics resources

Address of the bookmark: https://github.com/envgen

NCBI Datasets pages

BioStar — Wed, 12 Jul 2023 06:29:31 -0500

Update! Assembly and Genome record pages now redirect to new NCBI Datasets pages. NCBI Datasets is a new resource that makes it easier to find and download genome data. Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2023/07/11/ncbi-datasets-genome-assembly-pages/ #NCBICGR

Effective July 10, 2023, NCBI’s Assembly and Genome record pages now redirect to new NCBI Datasets pages. As previously announced, these updates are part of our ongoing effort to modernize and improve your user experience. NCBI Datasets is a new resource that makes it easier to find and download genome data.  

The following pages have been updated:

The NCBI Assembly record pages now redirect to the new NCBI Datasets Genome record pages that describe assembled genomes and provide links to related NCBI tools such as Genome Data Viewer and BLAST. 
The NCBI Genome record pages now redirect to the NCBI Datasets Taxonomy record pages that provide a taxonomy-focused portal to genes, genomes, and additional NCBI resources.

During this transition, you will have the option to return to the legacy Genome and Assembly record pages. We will remove the legacy pages in early 2024. 