BOL: Related items

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/

Bioinformatics Centre, Bose Institute vacancy of Research Associate / Senior Research Fellow

Mon, 22 Feb 2016 03:27:17 -0600

Bioinformatics Centre, Bose Institute vacancy of Research Associate / Senior Research Fellow

Location where with post of Research Associate / Senior Research Fellow is available:
Bioinformatics Centre, Bose Institute in Kolkata, West Bengal

Title of the Project: "Setting up of National Facility on Interactive Graphics Computer System".

No. of the Post: 01 One

Salary: Rs. 22000/- per month plus admissible HRA and Medical Benefits for RA and Rs. 20000/- per month plus admissible HRA and Medical Benefits for SRF (Extended).

Age Limit: Max. 35 years for RA and Max. 33 years for SRF (Extended)

Required Job Profile:

Candidate must possess PhD degree in biological or chemical sciences with in depth understanding of protein structure and function; experience on protein crystallization and various modeling software will be advantages and candidate who have submitted PhD thesis can be considered as extended SRF.

The project would involve cloning, expression, crustallization of vibrio cholera toxin, Ace and modeling of its admissible HRA and medical benefits for SRF (Extended).

How to apply:

Eligible and interested candidates should need to appear before the selection committee along with typed application addressed to the above mentioned address along with biodata with complete details and attested copies of certificates on 02.03.2016 at 11:30 am. No TA or DA will be paid for attending the interview. No TA or DA will be paid for attending the interview.

Refer to http://www.boseinst.ernet.in/ADVT/15/p_30.pdf

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

Bioinformatics Trainee at University of Kalyani

Tue, 22 Dec 2015 01:51:42 -0600

Bioinformatics Trainee
Eligibility : MSc
Location : Kolkata
Last Date : 28 Dec 2015
Hiring Process : Walk - In
University of Kalyani

Bioinformatics Trainee Job position in University of Kalyani
Number of Posts : 02
Qualification : M.Sc. in any branch of life science with prior knowledge of Bioinformatics
Fellowship / Stipend / Salary : As per DBT rules
Duration of the Post : Six months starting from January, 2016
How to apply
Walk-in-interview will be held on 28.12.2015 at Department of Biochemistry and Biophysics, University of Kalyani.

More at http://www.klyuniv.ac.in/index.php/recruitments

genomics public data links !

Jit — Thu, 13 Feb 2020 00:20:00 -0600

List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

Chekulaevalab

Tue, 12 Jan 2016 02:32:03 -0600

Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and role of non-coding RNAs in this process. Up to 90% of human DNA is estimated to be transcribed into so called non-coding RNAs that are not translated into proteins. Many of them act as potent modifiers of gene expression. miRNAs are a class of such short non-coding RNAs. They regulate expression of more than a half of eukaryotic genes, thus, affecting multiple biological processes, including cell proliferation, differentiation, apoptosis and senescence. Not surprisingly, miRNAs are involved in many human pathologies, including cancer and neurological disorders and hold great potential as drug targets, disease markers, as well as therapeutic agents.
Our lab is located at the Berlin Institute for Medical Systems Biology (BIMSB), a part of the Max Delbrück Center for Molecular Medicine (MDC).

http://www.chekulaevalab.org/

RA at University of Pune

Mon, 07 Mar 2016 03:48:33 -0600

Research Associate Job vacancies in University of Pune on temporary basis

No. of Post : 01

Department : Science and Technology

Qualifications : Ph.D. with specialization in Bioinformatics/Machine Learning/ Mathematical Biology/ Computational Biology/ Systems Biology with a minimum of 55% marks in M. Sc. (50% for candidates belongs to reserved category) or equivalent grade. Candidates who have submitted their Ph.D. thesis and are waiting for award of Ph.D. are also eligible. OR M. Sc. Bioinformatics with two years of research experience in the areas mentioned above, a minimum of 55% marks in M.Sc. (50% for candidates belongs to reserved categories) or equivalent grade and at least one publication in Science Citation Index (SCI) journal. Preference will be given to B.I.N.C. /J.R.F. /N.E.T. /S.E.T. qualified candidates.

Emoluments : Rs. 20,000/- (Including H.R.A.) per month.
How to apply

The complete application along with necessary documents and certificates should reach to 'The Director, Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Caneshkhind Road. Pune - 411 007 on or before 21st March, 2016 within official hours except Sundays (i.e. 10.20 am to 06.00 pm).

More at http://collegecirculars.unipune.ac.in/sites/documents/Job%20Openings/Forms/AllItems.aspx

Run miniasm assembler on nanopore reads !

Jit — Mon, 18 Dec 2017 04:07:50 -0600

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.

Find the detail of the reads repeats:

fq2fa ONT_A.fastq ONT_A.fasta

minimap2 -xava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf

awk '{if($1==$6){print}}' AONT.paf > AONTself.paf

awk '$5=="-"' AONTself.paf | awk '{print $1}'| sort|uniq > invertedrepeat.list

Generated a few palindrome and repeats plots (highlighting only repeats largest than 10, 20 and 30 kb)

minidot -f 5 -m 30000 AONTself.paf > AONTself30000.eps
sed 's/_template_pass_FAH31515//' AONTself30000.eps > AONTself30000final.eps

minidot -f 5 -m 20000 AONTself.paf > AONTself20000.eps
sed 's/_template_pass_FAH31515//' AONTself20000.eps > AONTself20000final.eps

minidot -f 5 -m 10000 AONTself.paf > AONTself10000.eps
sed 's/_template_pass_FAH31515//' AONTself10000.eps > AONTself10000final.eps

Assemble with miniasm:

miniasm -f ONT_A.fasta AONT.paf > AONT.gfa
grep '^S' AONT.gfa |awk '{print ">"$2"\n"$3}' > AONT_miniasm.fasta

minimap2 -xasm10 AONT_miniasm.fasta AONT_miniasm.fasta -t1 -X > AONT_miniasm.paf

awk '{if($1==$6){print}}' AONT_miniasm.paf > AONT_miniasm_self.paf

minidot -f 5 -m 10000 AONT_miniasm_self.paf > AONT_miniasm_self10000.eps

Njoy the assembly !

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/

Project Fellow Bioinformatics at Central University of Himachal Pradesh

Tue, 09 Feb 2016 03:58:00 -0600

Project Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics)

Location : Kulu

Last Date : 07 Mar 2016

Hiring Process : Face to Face Interview
Central University of Himachal Pradesh

Project Fellow Bioinformatics Job in Central University of Himachal Pradesh

Project (MRP) entitled: “A project proposal on targeting novel prokaryotic ubiquitin like post-translational modification pathway for therapeutic interventions against Mycobacterium tuberculosis” (No. MRP-MAJOR-MICR-2013-26840)

Essential Qualification: 1. Master degree in Bioinformatics/Biochemistry/Biotechnology/Environmental Science/Microbiology or any branch of Life Sciences with a minimum of 55% marks for general category (50% in case of SC/ST/PH) 2. UGC/CSIR NET, GATE qualified candidates will be given preference. Desirable Qualification: Experience in basic Bioinformatics and Molecular Biology techniques.

Age: Below 40 years as on 01/10/2015.

No.of Post: 1

Salary: NET/GATE qualified candidate: Rs. 16,000/-p.m. for initial two years and Rs. 18,000/- p.m. for the third year. Non-NET/GATE candidates: Rs. 14,000/-p.m. for initial two years and Rs. 16,000/-p.m. for the third year.

Mode of Selection: The selection shall be made on the basis of merit. The eligible candidates are required to appear for interview before the duly constituted Selection Committee for the purpose. The scheduled date, time and venue for the interview shall be intimated to the eligible candidates through phone/ e-mail.
How to apply

Last date for the receipt of applications is 07.03.2016.

More at http://www.cuhimachal.ac.in/news_all.aspx