BOL: Related items

Microscope

Jitendra Narayan — Fri, 04 Mar 2016 05:26:31 -0600

Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

Jit — Fri, 05 Jan 2018 04:12:20 -0600

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392)
is easy to install/run/configure
supports various types of dat
- HiSeq/MiSeq (100-500bp)
- Unitigs
- 454, ...

proovread maps high coverage data to pacbio reads (bwa mem, blasr, daligner) in multiple iterations.

Address of the bookmark: https://github.com/BioInf-Wuerzburg/proovread

PostDoc at IISER -TVM

Fri, 26 Feb 2016 03:53:05 -0600

Postdoctoral Fellowship/ Research Associateship

Eligibility : M Phil / Phd

Location : Thiruvananthapuram

Last Date : 30 Apr 2016

Hiring Process : Face to Face Interview
IISER -TVM

The Postdoctoral Fellowship/Research Associateship is a full-time, contractual position for highly qualified young scientists to carry out research at CCMS, IISER-TVM.

Research areas at the Centre

Quantum Chemistry/ Computational Fluid Dynamics/Condensed Matter Physics (Theory)/Genomics/Genetics/Gravitational Waves

Qualifications: PhD in Bioinformatics / Biophysics / Physics / Astrophysics / Chemistry / Mathematics / Engineering (Mechanical/Aerospace) Those who are in the final stages of their Ph.D. thesis submission are also eligible to apply. However, those candidates must have submitted the thesis at the time of the interview.

Experience: Applicants should have at least three peer reviewed publications and relevant experience in the research area they are applying for.

No. of positions: 5

Age limit: 35 yrs or below. A relaxation of 5 yrs will be applicable to candidates belonging to SC/ST/OBC and women candidates

Salary: The Fellowship carries a remuneration of INR Rs. 5,18,000 - Rs. 5,76,000 per annum (including HRA). The postdoctoral fellowship may not be held concurrently with any other national or international fellowships. It is also not transferable to any other fellowship
How to apply

Applications should reach the Head, CCMS, IISER Thiruvananthapuram,CET Campus, Engineering College PO,Thiruvananthapuram 695016 on or before April 30, 2016 by e-mail to ccms@iisertvm.ac.in by mentioning the research area name in the subject line.

More at http://www.iisertvm.ac.in/openings/read_opening/150.phpx

Project Assistant at IISER Mohali

Fri, 29 Jan 2016 11:04:27 -0600

Project Assistant Job position in Indian Institute of Science Education & Research (IISER) Mohali

Title : In silico understanding of molecular basis of recognition, binding, and regulation of mRNA by STAR family of transcriptional regulators.

No. of Post : 01

Department : Science and Technology

Qualifications : M.Sc./B.Tech in computational life sciences, computational chemistry, computational natural sciences or allied areas. Working experience in MD simulations, bioinformatics, molecular modeling, and drug designing is desirable and plus

Emoluments : As per DST norms
How to apply

Applicants are requested to send application along with bio-data and a summary of previous projects (if any) as a PDF file with the e-mail to Dr. Monika Sharma, Email: mnsharma@iisermohali.ac.in. Last date of applications is 17:00 IST. Feb 15, 2016. Shortlisted candidates will be called for interview on Feb 22, 2016.

More at http://14.139.227.202/tenders/tenderinvite/index.php/iiserm-project-openings/554-applications-are-invited-to-work-as-project-assistant-in-a-dst-inspire-research-project-funded-by-department-of-science-and-technology-india

shovill: Assemble bacterial isolate genomes from Illumina paired-end reads

BioStar — Sat, 02 Jan 2021 07:05:36 -0600

Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.

Address of the bookmark: https://github.com/tseemann/shovill

npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads

Shruti Paniwala — Mon, 11 Jun 2018 05:14:57 -0500

npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.

Address of the bookmark: http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html

flo

Jitendra Narayan — Wed, 10 Feb 2016 10:52:32 -0600

flo - same species annotations lift over pipeline

Lift over is the process of transferring annotations from one genome assembly to another. Usually lift over is done because there is a new, improved genome assembly for the species and good quality annotations (maybe manually curated or experimentally verified) are available on the old assembly.

The idea is simple: align the new assembly with the old one (e.g., with BLAT), process the alignment data to define how a coordinate or coordinate range on the old assembly should be transformed to the new assembly (e.g., as a chain file), transform the coordinates (e.g., with liftOver).

https://github.com/wurmlab/flo

Address of the bookmark: https://github.com/wurmlab/flo

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

Rahul Nayak — Fri, 19 Oct 2018 08:23:42 -0500

Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top–down manner. And along a guided tree, it iteratively merges sibling leaves in a bottom–up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data

Address of the bookmark: https://sourceforge.net/projects/bio-rainbow/files/

Project Assistant/ JRF at North Eastern Hill University

Fri, 12 Feb 2016 09:23:01 -0600

Project Assistant/ JRF

Eligibility : ME/M.Tech, Any Graduate, MSc

Location : Shillong

Last Date : 23 Feb 2016

Hiring Process : Face to Face Interview
North Eastern Hill University

Project Assistant/ JRF Jobs recruitment in North Eastern Hill University on temporary basis

Project Title : "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India"

Project Assistant

No. of Post : 01

Qualifications : Graduation

Desirable : Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

JRF

No. of Post : 01

Qualifications : M.Tech/M.Sc in Life Sciences/Botany/Biotechnology/ Bioinformatics;

Desirable : Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis
How to apply

The applications through email bicnehu@gmail.com or post must reach the Dr. Devendra Kumar Biswal, Co-Principal Investigator (Co-PI) within 15 days from the date of publication of this advertisement.

More at http://www.nehu.ac.in/Advertisements/projectVacancy.php

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

BioStar — Tue, 04 Feb 2020 23:23:16 -0600

Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.

Usage: perl run_rcorrector.pl [OPTIONS]
OPTIONS:
	Required
	-s seq_files: comma separated files for single-end data sets
	-1 seq_files_left: comma separated files for the first mate in the paried-end data sets
	-2 seq_files_right: comma separated files for the second mate in the paired-end data sets
	-i seq_files_interleaved: comma sperated files for interleaved paired-end data sets
	Optional
	-k INT: kmer_length (<=32, default: 23)
	-od STRING: output_file_directory (default: ./)
	-t INT: number of threads to use (default: 1)
	-trim : allow trimming (default: false)
	-maxcorK INT: the maximum number of correction within k-bp window (default: 4)
	-wk FLOAT: the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)
	-ek INT: expected number of kmers; does not affect the correctness of program but affects the memory usage (default: 100000000)
	-stdout: output the corrected reads to stdout (default: not used)
	-verbose: output some correction information to stdout (default: not used)
	-stage INT: start from which stage (default: 0)
		0-start from begining(storing kmers in bloom filter) ;
		1-start from count kmers showed up in bloom filter;
		2-start from dumping kmer counts into a jf_dump file;
		3-start from error correction.

Address of the bookmark: https://github.com/mourisl/Rcorrector/