BOL: Related items

Alignment-free sequence comparison tools available for next-generation sequencing data analysis

Abhimanyu Singh — Tue, 07 Nov 2017 05:33:33 -0600

kallisto

Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)

Software (C++)

https://pachterlab.github.io/kallisto/

Sailfish

Estimation of isoform abundances from reference sequences and RNA-seq data (k-mer based)

Software (C++)

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

Salmon

Quantification of the expression of transcripts using RNA-seq data (uses k-mers)

https://combine-lab.github.io/salmon/

RNA-Skim

RNA-seq quantification at transcript-level (partitions the transcriptome into disjoint transcript clusters; uses sig-mers, a special type of k-mers)

Software (C++)

http://www.csbio.unc.edu/rs/

Variant calling

ChimeRScope

Fusion transcript prediction using gene k-mers profiles of the RNA-seq paired-end reads

Software (Java)

https://github.com/ChimeRScope/ChimeRScope/wiki

FastGT

Genotyping of known SNV/SNP variants directly from raw NGS sequence reads by counting unique k-mers

Software (C)

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

Phy-Mer

Reference-independent mitochondrial haplogroup classifier from NGS data (k-mer based)

Software (Python)

https://github.com/danielnavarrogomez/phy-mer

LAVA

Genotyping of known SNPs (dbSNP and Affymetrix's Genome-Wide Human SNP Array) from raw NGS reads (k-mer based)

Software (C)

http://lava.csail.mit.edu/

MICADo

Detection of mutations in targeted third-generation NGS data (can distinguish patients’ specific mutations; algorithm uses k-mers and is based on colored de Bruijn graphs)

Software (Python)

http://github.com/cbib/MICADo

General mapper

Minimap

Lightweight and fast read mapper and read overlap detector (uses the concept of “minimazers”, a special type of k-mers)

Software (C)

https://github.com/lh3/minimap

Assembly

De novo genome assembly

MHAP

Produces highly continuous assembly (fully resolved chromosome arms) from third-generation long and noisy reads (10 kbp) using a dimensionality reduction technique MinHash

Software (Java)

https://github.com/marbl/MHAP

Miniasm

Assembler of long noisy reads (SMRT, ONT) using the Overlap-Layout Consensus (OLC) approach without the necessity of an error correction stage (uses minimap)

Software (C)

https://github.com/lh3/miniasm

LINKS

Scaffolding genome assembly with error-containing long sequence (e.g., ONT or PacBio reads, draft genomes)

Software (Perl)

https://github.com/warrenlr/LINKS/

Read clustering

afcluster

Clustering of reads from different genes and different species based on k-mer counts

Software (C++)

https://github.com/luscinius/afcluster

QCluster

Clustering of reads with alignment-free measures (k-mer based) and quality values

Software (C++)

http://www.dei.unipd.it/~ciompin/main/qcluster.html

Reads error correction

Lighter

Correction of sequencing errors in raw, whole genome sequencing reads (k-mer based)

Software (C++)

https://github.com/mourisl/Lighter

QuorUM

Error corrector for Illumina reads using k-mers

Software (C++)

https://github.com/gmarcais/Quorum

Trowel

Software (C++)

https://sourceforge.net/projects/trowel-ec/

Metagenomics

Assembly-free phylogenomics

AAF

Phylogeny reconstruction directly from unassembled raw sequence data from whole genome sequencing projects; provides bootstrap support to assess uncertainty in the tree topology (k-mer based)

Software (Python)

https://github.com/fanhuan/AAF

kSNP v3

Reference-free SNP identification and estimation of phylogenetic trees using SNPs (based on k-mer analysis)

Software (C)

https://sourceforge.net/projects/ksnp/files/

NGS-MC

Phylogeny of species based on NGS reads using alignment-free sequence dissimilarity measures d2* and d2 S under different Markov chain models (using k-words)

R package

http://www-rcf.usc.edu/~fsun/Programs/NGS-MC/NGS-MC.html

Species identification/taxonomic profiling

CLARK

Taxonomic classification of metagenomic reads to known bacterial genomes using k-mer search and LCA assignment

Software (C++)

http://clark.cs.ucr.edu/

FOCUS

Reports organisms present in metagenomic samples and profiles their abundances (uses composition-based approach and non-negative least squares for prediction)

Web service Software (Python)

http://edwards.sdsu.edu/FOCUS/

GSM

Estimation of abundances of microbial genomes in metagenomic samples (k-mer based)

Software (Go)

https://github.com/pdtrang/GSM

Mash

Species identification using assembled or unassembled Illumina, PacBio, and ONT data (based on MinHash dimensionality-reduction technique)

Software (C++)

https://github.com/marbl/mash

Kraken

Taxonomic assignment in metagenome analysis by exact k-mer search; LCA assignment of short reads based on a comprehensive sequence database

Software (C++)

https://ccb.jhu.edu/software/kraken/

LMAT

Assignment of taxonomic labels to reads by k-mers searches in precomputed database

Software (C++/Python)

https://sourceforge.net/projects/lmat/

stringMLST

k-mer-based tool for MLST directly from the genome sequencing reads

Software (Python)

http://jordan.biology.gatech.edu/page/software/stringMLST

Taxonomer

k-mer-based ultrafast metagenomics tool for assigning taxonomy to sequencing reads from clinical and environmental samples

Web service

http://taxonomer.iobio.io/

Other

d2-tools

Word-based (k-tuple) comparison (pairwise dissimilarity matrix using d2S measure) of metatranscriptomic samples from NGS reads

Software (Python/R)

https://code.google.com/p/d2-tools/

VirHostMatcher

Prediction of hosts from metagenomic viral sequences based on ONF using various distance measures (e.g., d2)

Software (C++)

https://github.com/jessieren/VirHostMatcher

MetaFast

Statistics calculation of metagenome sequences and the distances between them based on assembly using de Bruijn graphs and Bray–Curtis dissimilarity measure

Software (Java)

https://github.com/ctlab/metafast

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

DNA Nucleotide Counter

Neel — Fri, 12 Oct 2018 04:37:01 -0500

DNA Nucleotide Counter is delivered in a DNA Baser package together with other free molecular biology tools. Download the package and double click it. The programs inside the package will be extracted to the destination folder (specified by you). Go to the destination folder and double click the program you want to use.

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html

JRF/SRF at University of Calcutta

Fri, 31 Oct 2014 08:53:10 -0500

Applications are invited to appear at a walk-in-interview for one post of Junior Research Fellow in the DBT(DBT Twinning NER) sponsored project entitled “Protein folding kinetics is a selection force on shaping codon usage bias in the high expression genes” in the room of the HOD, Department of Biotechnology and the Coordinator, DR. B. C. Guha Centre for Genetic Engineering and Biotechnology, University College of Science, 35 Ballygunge Circular Road, Kolkata 700019 on the 12th November, 2014 at 3:00 p.m.

Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.

Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins

Emoluments: as per DBT norms

The project is tenable for two years, initially for one year.

Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)

Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.

No TA/DA is admissible for candidates appearing at the interview.

Dr. Rajat Banerjee
Assistant Professor
Department of Biotechnology and
Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology
University College of Science
35, Ballygunge Circular Road
Kolkata 700019

Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf

ENCODE3: A collection of research articles and related content describing the Encyclopedia of DNA Elements, its datasets and tools.

Shruti Paniwala — Sat, 08 Aug 2020 08:25:21 -0500

How cells, tissues and organisms interpret the information encoded in the genome has vital implications for our understanding of development, health and disease. Launched in 2003, the ENCyclopedia Of DNA Elements (ENCODE) project has the aim of mapping the functional elements in the human genome (later expanded to include model organisms).

During the first phase of ENCODE, published in 2007, microarray-based technologies were used to detect regions associated with transcription factors, certain histone modifications and open chromatin within a pre-specified 1% of the human genome.

ENCODE’s second phase saw a switch to sequencing-based technologies, the addition of new assay types and the analysis of functional elements genome-wide, described in a collection of research articles in 2012.

The Encyclopedia paper of ENCODE 3, published in Nature, gives an overview of the various assays that were performed in human and mouse cell lines and tissues and describes a Registry of human and mouse candidate cis-regulatory elements (cCREs).

More at https://www.nature.com/immersive/d42859-020-00027-2/index.html

Comparative genomics visualisation tools !

Neel — Thu, 17 Feb 2022 05:37:55 -0600

Comparative genomics visualisation tools !

Address of the bookmark: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&selected=%23BRIG&tag=Comparative

Opening for RA/extended SRF in Bioinformatics project by DBT at Bose Institute

Sun, 01 Mar 2015 00:50:18 -0600

The institute has evolved over the years into a multi-disciplinary research organization with stress on fundamental research in its pursuit of advancement of knowledge in Science and technology and at the same time developing highly competent and able scientific manpower for the country. The institute has on its staff highly qualified and experienced scientists working in the field of Biological, biochemical, Chemical and Physical sciences placed in long established departments of Physics, Chemistry, Botany, Microbiology, Biochemistry, and Biophysics, and the research sections on plant Molecular & Cellular Genetics, Animal Physiology, Immunotechnology and Environmental science

Walk-in-Interview will be held on 04th March 2015 at 11.30 A.M. in the Bio- Informatics Centre of Bose Institute, P-1/12, C.I.T. Scheme VII-M, Kolkata- 700054 for two (02) positions of Research Associate/ Extended Senior Research Fellow in the DBT sponsored following two projects running under the CoE- Bioinformatics under the guidance of Prof. Pinakpani Chakrabarti, Bioinformatics Centre.

Position : RA/SRF
Project title : 1. "Centre of Excellence (CoE) in Bioinformatics at Bose Institute”,2. Project entitled “Setting up of National Facility on Interactive Graphysics Computer System (IGCS) for Biomolecular Modeling, Molecular Dynamics & Structures”

Desired Profile : Ph.D degree in Biological or Chemical Sciences with in-depth understanding of protein structure and dynamics for R.A. position.Those who have submitted thesis can be considered for Extended SRF position
Preferred : Knowledge of computer programming and bioinformatics softwares.
Stipend : For R.A- Rs. 22,000/- p.m., plus admissible H.R.A. and Medical benefit. For Extended SRF - Rs. 20,000/- p.m., plus admissible H.R.A.and Medical benefit.
Age : For R.A- Below 35 years; For Extended SRF - Below 33 years
Interested and eligible candidates should appear before the Selection Committee with atyped application addressed to the Sr.Prof. & In-Charge, Registrar's Office, Bose Institute, P- 1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 along with Bio-data giving details of qualification i.e. examination passed, year, division, percentage of marks from Secondary onwards with attested copies of Certificates, Mark-Sheet and testimonials. The candidates should also bring the original mark-sheets, certificates etc. at the time of Interview.

Walk in Interview : 04.03.15

More at http://www.boseinst.ernet.in/ADVT/14/p_34.pdf

Research Associate Biotechnology/JRF/Lab. Assistant Indian Institute of Vegetable Research (IIVR) - Varanasi, Uttar Pradesh

Wed, 11 Mar 2015 08:59:27 -0500

F. No.: 2-19/2011-Adm.I

Research Associate Biotechnology /JRF / Lab. Assistant recruitment in Indian Institute of Vegetable Research

Project:
Genomics assisted selection of Solanum chilense introgression lines for enhancing drought tolerance in tomato
Post Name : Research Associate
Qualification : Ph.D in Biotechnology/ Bioinformatics/Genetics & Plant Breeding. M. Tech in Computer Science with at least one research paper in science citation indexed journal. Desirable: Experience in bioinformatics and next generation sequence data handling. Familiarity in Linux, R, Perl/Phython or other programming languages. Willingness to travel to European partner centers.

Pay Scale : Rs. 36000 for 1st and 2nd year as per rules for Research Associate. Rs. 25000/- for 1st and 2nd year and Rs. 28000 as per rules for Junior Research Fellow. Rs. 7000/- for Lab. Assistant.

Age : Not more than 35 years for Men and 40 years for Women (Relaxable for SC/ST/OBC/PH candidates as per rules) for Research Associate/ Junior Research Fellow. Minimum age will be 21 years and maximum age will be 45 years (Relaxable for SC/ST/OBC/PH candidates as per rules) for Lab.Assistant.

More at http://iivr.org.in/Job%20Oppurtunities/RA20.03.2015.pdf

Alessandra Carbone Lab

Tue, 26 May 2015 08:54:34 -0500

Our group works on various problems connected with the functioning and evolution of biological systems. We use mathematical tools, coming from statistics and combinatorics, algorithmic tools and molecular physics tools to study basic principles of cellular functioning starting from genomic data. We run several projects in parallel, all aiming at understanding the basic principles of evolution and co-evolution of molecular structures in the cell. They are intimately linked to each other.

Our main research themes are:

Domain annotation and metagenomics
Transcriptomics and sequence analysis
Protein evolution and interactions
Protein conformational dynamics

More at http://www.lcqb.upmc.fr/AnalGenom/home.html

X. Shirley Liu Lab

Tue, 26 May 2015 17:28:23 -0500

The research in our laboratories are focused on the following three areas:

Bioinformatics
Cancer
Epigenetics

More at http://liulab.dfci.harvard.edu/