BOL: Related items

Liftoff: an accurate tool that maps annotations in GFF or GTF between assemblies

Jit — Tue, 30 Jun 2020 21:40:52 -0500

Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome.

Address of the bookmark: https://github.com/agshumate/Liftoff

VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.

biogeek — Tue, 25 Aug 2020 03:40:17 -0500

VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.

http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf

Address of the bookmark: https://www.broadinstitute.org/viral-genomics/vicuna

Ventoy: an open source tool to create bootable USB drive

LEGE — Tue, 29 Jun 2021 10:16:19 -0500

Ventoy is an open source tool to create bootable USB drive for ISO/WIM/IMG/VHD(x)/EFI files. With ventoy, you don't need to format the disk over and over, you just need to copy the image files to the USB drive and boot it. You can copy many image files at a time and ventoy will give you a boot menu to select them. x86 Legacy BIOS, IA32 UEFI, x86_64 UEFI, ARM64 UEFI and MIPS64EL UEFI are supported in the same way. Both MBR and GPT partition style are supported in the same way. Most type of OS supported(Windows/WinPE/Linux/Unix/Vmware/Xen...) 700+ ISO files are tested.

Address of the bookmark: https://github.com/ventoy/Ventoy

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Jit — Wed, 29 Jun 2022 03:22:26 -0500

InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/

Minda: a tool for evaluating structural variant (SV) callers

LEGE — Sun, 31 Mar 2024 02:43:50 -0500

Minda is a tool for evaluating structural variant (SV) callers that

standardizes VCF records for compatibility with both germline and somatic SV callers,
benchmarks against a single VCF input file, or
benchmarks against an ensemble call set created from multiple VCF input files.

Address of the bookmark: https://github.com/KolmogorovLab/minda

LoVis4u: Locus Visualisation tool for comparative genomics

LEGE — Tue, 17 Sep 2024 02:30:57 -0500

Description

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u

FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)

Jit — Fri, 13 Jul 2018 17:27:01 -0500

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Its underlying procedure follows a similar workflow as described by Goris et al. 2007. However, it avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and alignment identity estimates. Based on our experiments with complete and draft genomes, its accuracy is on par with BLAST-based ANI solver and it achieves two to three orders of magnitude speedup. Therefore, it is useful for pairwise ANI computation of large number of genome pairs. More details about its speed, accuracy and potential applications are described here: "High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries".

Address of the bookmark: https://github.com/ParBLiSS/FastANI

wgd—simple command line tools for the analysis of ancient whole-genome duplications

LEGE — Thu, 23 Jul 2020 05:49:45 -0500

wgd is a easy to use command-line tool for K_S distribution construction named wgd. The wgd suite provides commonly used K_S and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

Phased Human Genome Assembly !

Rahul Nayak — Mon, 08 Oct 2018 09:10:54 -0500

The new publicly available assembly (PacBio HG00733) has the fewest gaps of any human genome assembly, with more than half of the genome contained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with PacBio data generated with the company’s Sequel® System. Using the FALCON-Unzip assembler, maternal and paternal haplotypes were resolved over more than 80% of the genome. Maternal and paternal haplotype blocks were then further phased using Hi-C technology and the FALCON-Phase methoddeveloped in collaboration with Phase Genomics. The genome was then de novo scaffolded using Phase Genomics’ Proximo Hi-C platform, resulting in the first chromosome-scale diploid assembly of a single individual accomplished with only two technologies. More specific details about the assembly are included on the PacBio blog.

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
BioReport Podcast on the value of ethnic-specific reference genomes
Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
Webinar: Assembling High-Quality Human Reference Genomes for Global Populations
FALCON-Phase press release and article preprint
PacBio research focus webpage about Human Population Genetics

Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

Carefully opt for human reference genome

biogeek — Tue, 18 Feb 2020 07:43:32 -0600

Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use