BOL: Related items

Biggest Human Brain Project (HBP) launched!!!

Rahul Agarwal — Mon, 07 Oct 2013 19:50:55 -0500

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs

List of bioinformatics companies and genomics service providers

Rahul Agarwal — Wed, 02 Apr 2014 06:52:28 -0500

Plz check out link for bioinformatics and genomics companies.

Address of the bookmark: http://grouthbio.com/Genome_Software_Service.php

The Minerva Research Group for Bioinformatics

Tue, 27 May 2014 15:48:14 -0500

The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

GOLD:Genomes Online Database

Jit — Wed, 26 Jul 2017 07:49:29 -0500

GOLD:Genomes Online Database, is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world.

https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Jit — Tue, 26 Dec 2017 22:23:39 -0600

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

Address of the bookmark: https://ncbi.github.io/magicblast/

HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads

Rahul Nayak — Tue, 08 May 2018 04:27:22 -0500

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): Theory and Application,

Jit — Wed, 23 May 2018 06:54:32 -0500

BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion error.

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you.

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

SimLoRD: A read simulator for third generation sequencing reads

Aaryan Lokwani — Wed, 22 Aug 2018 10:40:27 -0500

SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.

Reads are simulated from both strands of a provided or randomly generated reference sequence.

The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)
The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length
Quality values and number of passes depend on fragment length.
Provided subread error probabilities are modified according to number of passes
Outputs reads in FASTQ format and alignments in SAM format

Address of the bookmark: https://bitbucket.org/genomeinformatics/simlord/

Qualimap2: Evaluating next generation sequencing alignment data

Jit — Tue, 11 Sep 2018 04:44:29 -0500

Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Supported types of experiments include:

Whole-genome sequencing
Whole-exome sequencing
RNA-seq (speical mode available)
ChIP-seq

Address of the bookmark: http://qualimap.bioinfo.cipf.es/

sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)

Jit — Tue, 13 Nov 2018 07:25:38 -0600

Required python modules

biopython
intervaltree
numpy
scipy
tqdm
PyYAML

Address of the bookmark: https://github.com/cerebis/sim3C