BOL: Related items

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/

Shouji: a fast and efficient pre-alignment filter for sequence alignment

Jit — Mon, 04 Nov 2019 07:09:45 -0600

The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes.

We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator design that adopts modern FPGA (field-programmable gate array) architectures to further boost the performance of our algorithm.

More at https://github.com/CMU-SAFARI/Shouji

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

AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Jit — Sat, 01 Feb 2020 13:38:49 -0600

AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler

LEGE — Thu, 09 Jul 2020 03:13:06 -0500

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:

single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
paired-end single-cell RNA-seq (strand-specific/agnostic)
nanopore RNA-seq (PCR cDNA/direct cDNA/direct RNA)

Written by Ka Ming Nip ✉️

Address of the bookmark: https://github.com/bcgsc/RNA-Bloom

MMseqs2: ultra fast and sensitive sequence search and clustering suite

Abhi — Wed, 06 Oct 2021 07:01:14 -0500

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments

LEGE — Mon, 22 Sep 2025 23:51:02 -0500

termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

Fourth Branch of Life

Jitendra Narayan — Mon, 09 Sep 2013 21:48:37 -0500

Scientist have found the biggest viruses known, pandoraviruses which opened up entirely /completely... new questions questions and raise objections to in science. It even suggesting a fourth domain of life.

The new visrus are about one micron—a thousandth of a millimeter—in length, the newfound genus Pandoravirus dwarfs other viruses, which range in size from about 50 nanometers up to 100 nanometers. A genus is a taxonomic ranking between species and family.

Find more at @ http://www.nature.com/scitable/blog/viruses101/newly_found_pandoraviruses_hint_at

http://news.nationalgeographic.co.uk/news/2013/07/130718-viruses-pandoraviruses-science-biology-evolution/

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

Mosquito species known for transmitting the Dengue virus

BioStar — Wed, 03 Apr 2024 00:05:51 -0500

Here is a list of mosquito species known for transmitting the Dengue virus along with essential and applied information about each species:

1. Aedes aegypti:
- Geographical Distribution: Found in tropical and subtropical regions worldwide.
- Biting Behavior: Daytime biter, prefers feeding indoors, often around human dwellings.
- Role in Dengue Transmission: Primary vector responsible for transmitting Dengue virus to humans.

2. Aedes albopictus (Asian tiger mosquito):
- Geographical Distribution: Found in tropical, subtropical, and temperate regions worldwide.
- Biting Behavior: Daytime biter, feeds both indoors and outdoors, aggressive feeder.
- Role in Dengue Transmission: Secondary vector, can transmit Dengue virus to humans.

3. Aedes polynesiensis:
- Geographical Distribution: Found in Pacific Islands and coastal regions.
- Biting Behavior: Daytime biter, prefers feeding outdoors, often near coastal areas.
- Role in Dengue Transmission: Vector of Dengue virus in specific geographic regions.

4. Aedes scutellaris:
- Geographical Distribution: Found in Southeast Asia, Pacific Islands, and coastal regions.
- Biting Behavior: Daytime feeder, active in shaded areas, prefers outdoor environments.
- Role in Dengue Transmission: Vector of Dengue virus, particularly in coastal areas.

5. Aedes africanus:
- Geographical Distribution: Found in parts of Africa, including forested areas.
- Biting Behavior: Daytime feeder, prefers shaded areas, bites humans and other animals.
- Role in Dengue Transmission: Vector of Dengue virus in African regions.

Understanding the geographical distribution and biting behavior of these mosquito species is crucial for implementing effective control and prevention strategies to reduce Dengue virus transmission.

Influenza animation - flu virus mechanism

Thu, 17 Oct 2013 19:43:13 -0500

Animation of the mechanism of an influenza virus and how Crucell's antibodies target the HA1 proteins on the virus and prevent further spread of influenza. Client: Crucell Direction, Design & Animation: Daniel Lim, 2Preform Music & Sound Design: Javier Barrero, Logical Disorder Production Company: David Hager, All Terrain Media