BOL: Related items

EAGLER: a scaffolding tool for long reads.

Jit — Mon, 04 Jun 2018 05:26:03 -0500

EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nanopore reads.

The tool should be compatible with most UNIX flavors and has been successfully tested on the following operating systems:

Mac OS X 10.11.1
Mac OS X 10.10.3
Ubuntu 14.04 LTS

https://bib.irb.hr/datoteka/844447.Diplomski_2015_Luka_terbi.pdf

Address of the bookmark: https://github.com/mculinovic/EAGLER

Download blasr 1.3 version

Jit — Fri, 15 Jun 2018 03:01:20 -0500

DOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr

I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error:

fail to open file './temporarySam'

[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 161.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70989574 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 30 all_p_ctg.fa -
[main] Real time: 2402.523 sec; CPU: 53429.488 sec
[E::hts_open_format] Failed to open file temporarySam
samtools sort: can't open "temporarySam": No such file or directory
[bwa_aln_core] convert to sequence coordinate... 1.00 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... PREPROCESS:
Fastq format is recognized
[Thu Jun 14 18:16:47 2018] Building bwa index...
bwa index -p all_p_ctg.fa /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa
[Thu Jun 14 18:18:35 2018] Finding the SA coordinates of the reads using BWA aln...
[Thu Jun 14 18:58:37 2018] Generate alignments of reads using bwa sampe...
bwa samse -n 1 all_p_ctg.fa read.sai - | grep '\(^@\|XT:A:U\)' | /usr/local/bin/samtools view -S -h -b -F 0x4 - | /usr/local/bin/samtools sort -@ 20 -no - temporarySam > FALCON-Unzip-Scaff.bam
Mapping long-reads using blasr...
/home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr -nproc 40 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > FALCON-Unzip-Scaff.map
sh: 1: /home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr: Permission denied
Sorting mapping results...
sort -k1,1 -k9,9g FALCON-Unzip-Scaff.map > FALCON-Unzip-Scaff.map.sort
Analyzing sorted results...
Extracting linking information...
i3 2000 5000
i2 1000 2000
i4 5000 15000
i0 -200 300
i5 15000 40000
i1 300 1000
Repeat detection...
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2
Illegal division by zero at /home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl line 93.
readline() on closed filehandle FILE at bin/OPERA-long-read.pl line 250.
rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai
rm: cannot remove 'anchor_contig_info.dat': No such file or directory
mv FALCON-Unzip-Scaff.bam FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_repeat.pl FALCON-Unzip-Scaff-with-repeat.bam repeat.dat | /usr/local/bin/samtools view - -h -S -b > FALCON-Unzip-Scaff.bam
rm FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin/OPERA-LG config > log
Analyzing 1 library: FALCON-Unzip-Scaff.bam
min library mean : 0
minimum contig length is 500
Current library: 1 out of 7
Analyzing file: pairedEdges_no_repeat_i0
Analyzing file: pairedEdges_no_repeat_i1
Analyzing file: pairedEdges_no_repeat_i2
Analyzing file: pairedEdges_no_repeat_i3
Analyzing file: pairedEdges_no_repeat_i4
Analyzing file: pairedEdges_no_repeat_i5
ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta

To resolve this, try downloading blasr version 1.3 above and re-run :)

Converting a VCF into a FASTA given some reference !

Jit — Fri, 20 Jul 2018 10:03:53 -0500

Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

JRF/SRF at Jawaharlal Nehru Institute ofAdvanced Studies (JNIAS), Hyderabad

Fri, 31 Oct 2014 08:48:23 -0500

Applications for Academic Projects in Biotechnology, Bioinformatics, Environmental Sciences and Computer Science & Engineering

About JNIAS
Jawaharlal Nehru Institute of Advanced Studies (JNIAS), Hyderabad has been established by Dr. D. Swaminadhan Research Foundation (DSRF), Hyderabad as a Research and Educational Institution with a view to contribute in developing advanced technologies and build „core competence‟ in specific areas. The activities of JNIAS involves: Education, Research Training and Innovations in the fields of Sciences, Technologies, Humanities and Social Sciences. It aims to blossom into an Advanced Institute of education and research with a reservoir of expertise and experience in the relevant fields and the necessary capability to harness multi-disciplinary research and studies. JNIAS has been recognized as an Advanced Research Institute by Jawaharlal Nehru Technological University Hyderabad (JNTUH), Hyderabad and Jawaharlal Nehru Technological University Anantapur (JNTUA), for offering Ph.D., P.G M.Phil, P.G Diploma and Training Programmes in Sciences and Engineering & Technology.

Jawaharlal Nehru Architecture and Fine Arts University (JNAFAU) Hyderabad also recognized JNIAS for offering UG, PG degree in Architecture.

Projects & Facilities

JNIAS offers wide range of projects:

Biotechnology area:

Molecular Biology
Microbiology
Nanotechnology
Bioinformatics (Schrodinger Software)
In Silico studies & Drug Designing
Sequence analysis
Protein structure function studies

Registration
Tuition Fees: Interested students need to pay the following tuition fees:
1. Six Month’s Project: Rs. 20,000/-
2. Four Month’s Project: Rs. 15,000/-
3. Three Month’s Project: Rs. 10,000/-
4. One Month - Hands on Training : Rs. 8,000/-

For enquires call:
91-7893203414 (Biotechnology), 91-9949582263 (Environmental Sciences) 91-8977369305 (Computer Science)

Interested student may download the application from the website (www.jnias.in) and send the hard copy of the completed application forms and Curriculum Vitae along with the Demand Draft drawn on any nationalized Banks in favor of “The Registrar, JNIAS, Secunderabad”. Application forms can be sent through email to academicprojects@jnias.in

Address
Jawaharlal Nehru Institute of Advanced Studies (JNIAS)
6th Floor, Buddha Bhavan, M.G Road,
Secunderabad - 500 003
Andhra Pradesh, India
Tele/Fax: 040- 27541551; 27541553
Mobile: 08885541554
Web site: www.jnias.in

Brochure : https://drive.google.com/file/d/0B3zPwhgA-u-nU0dyMFd2OWcxNUpSTWNYc0xDSGs5UDI4UDNB/view?usp=sharing

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly

Rahul Nayak — Thu, 14 May 2020 15:09:52 -0500

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm in BWA package. In the package, we provided a compiled bwa, so the user needn't to install bwa. LR_Gapcloser uses the alignments to find the bridging that cross the gap, and then fills the long read original sequence into the genomic gaps.

Address of the bookmark: https://github.com/CAFS-bioinformatics/LR_Gapcloser

Google Genomics

Reshma Khatun — Fri, 17 Oct 2014 02:14:14 -0500

Google Genomics provides an API to store, process, explore, and share DNA sequence reads, reference-based alignments, and variant calls, using Google's cloud infrastructure.

Store alignments and variant calls for one genome or a million.
Process genomic data in batch by running principal component analysis or Hardy-Weinberg equilibrium, in minutes or hours, by using parallel computing frameworks like MapReduce.
Explore data by slicing alignments and variants by genomic range across one or multiple samples -- for your own algorithms or for visualization; or interactively process entire cohorts to find transition/transversion ratios, allelic frequency, genome-wide association and more using BigQuery.
Share genomic data with your research group, collaborators, the broader community, or the public. You decide.

Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

Research Scientist – National Institute of Cholera and Enteric Diseases

Wed, 22 Oct 2014 10:26:46 -0500

The following post is to be filled up on purely temporary basis under the project entitled "Second phase of Task Force Biomedical Informatics Center of ICMR" under Dr. Santasabuj Das, Scientist 'D' of this Institute:-

01. Scientist II 01
Essential: Ph.D. degree in Life Sciences from a recognized university along with a minimum of 2 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

OR
Ph.D. degree in Bioinformatics from a recognized university.

OR
M.Sc. in Bioinformatics from a recognized university along with a minimum of 3 years of research experience in Bioinformatics as evidenced by publications in the peer reviewed journals.

Desirable:
Thorough Knowledge about In silico genome analysis and comparative genomics.
Experience with in silico identification of novel virulence factors of pathogens, host-pathogen interactions and Systems Biology.
Additional Postdoctoral research experience in relevant subjects from a recognized institutions.

Rs. 44,000/- p.m. (consolidated) plus 30% HRA

Below 40 years

Applications along with Bio-Data containing detail work experience and full list of publications may be sent via email tosantasabujdas@yahoo.com latest by October 27, 2014.

Short-listed candidates will be called via email for an interview to be held at the institute in the second week of November, 2014.

Advertisement: www.niced.org.in/placements.htm

Synima: a Synteny imaging tool for annotated genome assemblies

Abhimanyu Singh — Tue, 30 Oct 2018 10:49:13 -0500

Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Address of the bookmark: https://github.com/rhysf/Synima

Celebrating Crystallography - An animated adventure

Fri, 31 Oct 2014 15:59:00 -0500

NEW: Now with French or Spanish subtitles (click on the 'Captions' icon to select). Plus... Watch the French language version here: https://www.youtube.com/watch?v=PvLu7BOsJhM X-ray crystallography is arguably one of the greatest innovations of the twentieth century, but not that many people know what it is or how it came about. Join us on an animated journey through the 100 year history of crystallography -- from the pioneering work of William and Lawrence Bragg in 1913 to the surface of Mars! Narrated by structural biologist Stephen Curry and produced by animation company 12foot6, the film explores the extraordinary history of crystallography. To date 28 Nobel Prizes have been awarded to projects related to the field and X-ray crystallography remains the foremost technique in determining the structures of a huge range of complex molecules. This film was produced in celebration of the Bragg Centenary and was funded by STFC. Watch more science videos on the amazing Ri Channel: http://richannel.org Watch more animations from 12foot6: http://12foot6.com/ The Ri is on Twitter: http://twitter.com/ri_science and Facebook: http://www.facebook.com/royalinstitution Subscribe for the latest science videos: http://richannel.org/newsletter

ANItools web: a web tool for fast genome comparison within multiple bacterial strains

Jit — Wed, 14 Nov 2018 04:34:23 -0600

ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nucleotide identity (ANI), you could download and run this program directly. Or you could send us the genome sequence by email. Then we will do the analysis work for you.

https://academic.oup.com/database/article/doi/10.1093/database/baw084/2630454

Address of the bookmark: http://ani.mypathogen.cn/