BOL: Related items

Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data

Jit — Tue, 22 Jan 2019 06:26:55 -0600

Run a pipeline processing fast5s to a consensus in a single command.
Recommended fixed "standard" and "fast" pipelines.
Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath.
Seemless distribution of tasks over local or distributed compute.
Highly configurable.
Open source (Mozilla Public License 2.0).

Documentation can be found at https://nanoporetech.github.io/katuali/.

Address of the bookmark: https://github.com/nanoporetech/katuali

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

Sequencing Solutions to World Health

Rahul Agarwal — Thu, 29 Aug 2013 15:05:35 -0500

"New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

Two major breakthrough!!

Rahul Agarwal — Mon, 02 Sep 2013 10:18:11 -0500

"Scientists in Uruguay in colloboration with European partners sequenced the genome of the high-value Tannat grape, from which "the most healthy of red wines" are fermented.

A quick, $1 syphilis test in development by researchers from UNU-BIOLAC."

Source:

http://www.sciencedaily.com/releases/2013/09/130902101846.htm

http://www.eurekalert.org/pub_releases/2013-09/tca-ssg082613.php

Encode sequencing data freely available to download and use for academic means

Rahul Agarwal — Thu, 13 Mar 2014 18:18:08 -0500

In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).

More information:

https://genome.ucsc.edu/ENCODE/pilot.html

Address of the bookmark: https://genome.ucsc.edu/ENCODE/

New RNA Seq tool

Rahul Agarwal — Fri, 25 Apr 2014 10:59:04 -0500

"By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy."

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/