BOL: Related items

SIMBA: a Genome Assembly Project Management System

Neel — Thu, 29 Nov 2018 08:52:25 -0600

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

Address of the bookmark: http://ufmg-simba.sourceforge.net/

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Neel — Sun, 13 Jan 2019 07:03:25 -0600

A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section

Address of the bookmark: https://gvolante.riken.jp/analysis.html

Caulobacter ethensis - 2.0 : Computer-generated Genome of a Living Organism

Abhimanyu Singh — Wed, 03 Apr 2019 08:45:22 -0500

All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0.

It is the world's first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich.

However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.

Source: https://www.sciencedaily.com/releases/2019/04/190401171343.htm

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Jit — Tue, 06 Aug 2019 21:37:56 -0500

gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and transcriptome assemblies.

Address of the bookmark: https://gvolante.riken.jp/

Genome Informatics Section Lab !

Sat, 25 Jan 2020 06:38:23 -0600

Our section develops and applies computational methods for the analysis of massive genomics datasets, focusing on the challenges of genome sequencing and comparative genomics. We aim to improve such foundational processes and translate emerging genomic technologies into practice.

The Genome Informatics Section is hiring! Come join our outstanding team at the NIH’s National Human Genome Research Institute and contribute to the development of new reference genomes and computational methods for DNA sequencing and analysis. Both postdoc and PhD students positions are available. More information and application instructions follow below.

More at https://genomeinformatics.github.io/

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

Simons Genome Diversity Project

Jit — Sat, 08 May 2021 21:55:25 -0500

Complete genome sequences from more than one hundred diverse human populations

All genomes in the dataset were sequenced to at least 30x coverage using Illumina technology. The sequencing reads were mapped and genotyped using a customized procedure that was optimized for population genetic analysis. The researchers eliminated bias of alleles toward matching the human genome reference sequence, and determined genotypes on a single-sample basis to avoid preferential calling of genotypes from populations that had more individuals represented.

Address of the bookmark: https://www.simonsfoundation.org/simons-genome-diversity-project/

HISAT2 Index Files Download !

LEGE — Wed, 15 Sep 2021 22:17:49 -0500

Resource for downloading all the HISAT2 related files

Please cite:

Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). https://doi.org/10.1038/s41587-019-0201-4

Address of the bookmark: http://daehwankimlab.github.io/hisat2/download/#h-sapiens

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

KAST

Neel — Wed, 23 Feb 2022 08:28:36 -0600

Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST