BOL: Related items

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

BioJoker — Tue, 02 Apr 2019 21:54:55 -0500

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Jit — Wed, 13 Nov 2019 22:20:19 -0600

mosdepth can output:

per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.
mean per-window depth given a window size--as would be used for CNV calling.
the mean per-region given a BED file of regions.
a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.
quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)
threshold output to indicate how many bases in each region are covered at the given thresholds.
A summary of mean depths per chromosome and within specified regions per chromosome.

Address of the bookmark: https://github.com/brentp/mosdepth

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads

Jit — Tue, 28 Jan 2020 03:27:33 -0600

FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.

http://bioinfo.ut.ee/FastGT/

https://github.com/bioinfo-ut/GenomeTester4/

Address of the bookmark: http://bioinfo.ut.ee/FastGT/

HASLR: a hybrid assembler which uses both second and third generation sequencing reads

BioStar — Mon, 04 May 2020 02:04:03 -0500

HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

Address of the bookmark: https://github.com/vpc-ccg/haslr

Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data

Jit — Thu, 11 Feb 2021 21:39:05 -0600

Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz v1.2.7 for Linux x86_64 system. If you could not run it (which is usually caused by low version of libc++ or libz library) or you want to build a version optimized for your system, you can re-compile the programs:

user@linux$ make clean && make

Address of the bookmark: https://github.com/hellosunking/Ktrim

Queensland Centre for Medical Genomics, Grimmond Lab

Sun, 14 Jul 2013 11:58:34 -0500

Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

Lateral Gene Transfer Is Enriched in Cancer Samples

Jitendra Narayan — Mon, 22 Jul 2013 05:13:06 -0500

There has been always a confusion on cancer and bacteria relationship. This is the first paper which shows lateral gene transfer causes cancer.

Find more at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003107

Cancers cure is on the way !!!

Jit — Wed, 22 Jan 2014 12:00:46 -0600

The study on blind mole rat (Spalax) was carried out by researchers from the University of Haifa, Israel, and published in the peer-reviewed scientific journal BMC Biology.

The blind mole rat (Spalax) is an intriguing creature worthy of study. This was animal research examining the resistance subterranean blind mole rats (Spalax) have to cancers. Blind mole rats are one of a unique group of animals that spend their lives underground, are tolerant of very low oxygen levels (down to only 3% concentration – levels that would kill a human), have a long lifespan of more than 20 years, which is exceptional for a small rodent, and show no clear signs of ageing or age-related diseases.

This research has demonstrated the unique abilities of the blind mole rat to resist cancer, even when directly given potent cancer-causing chemicals. In this study researchers gave blind mole rats potent cancer-causing chemicals either through injections or applied directly to the skin, but the animals didn't develop cancer.

Remarkably, connective tissue cells (fibroblasts) taken from the blind mole rat even prevented the growth of human cancer cells when they were grown together in the laboratory.

In the laboratory, the researchers also demonstrated how connective tissue cells called fibroblasts taken from the animal seem to play an important role in this cancer resistance. These cells prevented the growth of human cancer cells when the two types of cells were grown together in the laboratory.

The researchers concluded that, "This report provides pioneering evidence that Spalax [the blind mole rat] is not only resistant to spontaneous cancer, but also to experimentally induced cancer, and shows the unique ability of Spalax fibroblasts to inhibit growth and kill cancer cells, but not normal cells, either through direct fibroblast-cancer cell interaction or via soluble factors."

Nonetheless, there remains optimism that understanding the anti-cancer mechanisms of mole rats may one day help inform further cancer treatments for humans, but a lot more research – and probably a significant amount of time – is needed before this can be considered.

Reference:

Image: telegraph.co.uk

http://www.biomedcentral.com/1741-7007/11/91

Manov, Irena, et al. "Pronounced cancer resistance in a subterranean rodent, the blind mole-rat, Spalax: in vivo and in vitro evidence." BMC biology 11.1 (2013): 91.

http://www.nhs.uk/news/2014/01January/Pages/Claims-of-a-universal-cure-for-cancer-misleading.aspx

http://www.express.co.uk/news/health/454188/EXCLUSIVE-Cure-for-ALL-cancers-is-on-the-way-as-scientists-discover-major-breakthrough

http://www.dailymail.co.uk/health/article-2540321/Could-mole-rats-hold-key-cure-cancer-Scientists-hail-potentially-life-changing-breakthrough.html

Cancer research database

Neel — Tue, 01 Sep 2015 17:36:31 -0500

Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.

The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.

The Cancer Gene Markers Database (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.

The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States’ National Center for Biotechnology Information and the Kyoto Encyclopedia of Genes and Genomes. It also includes experimental data from PubMed.

In a paper published last month in Nature Scientific Reports, the researchers from SVU’s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.

RATT

Jitendra Narayan — Sun, 07 Feb 2016 16:09:40 -0600

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

Address of the bookmark: http://ratt.sourceforge.net/