BOL: Related items

BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data between different formats.

Jit — Mon, 13 Jun 2016 05:47:21 -0500

Reformatis a member of the BBMap/BBTools package. It is a multipurpose tool designed for converting reads or other nucleotide data between different formats. It supports, and can inter-convert:

fastq
fasta
fasta+qual
sam
scarf (an old Illumina format)
bam (if samtools is installed)
gzip
zip
ascii-33 (sanger)
ascii-64 (old Illumina)
paired files
interleaved files

It is multithreaded and can process data at over 500 megabytes per second, and can accept streams from standard in and write to standard out, allowing it to be easily dropped into the middle of a pipeline for format conversion. Reformat autodetects formats based on file extensions and content, making it very easy to use; and the autodetection can be overridden, allowing flexibility for people who don't like to follow naming conventions, or out-of-spec fastq files with qualities values like -17 or 120.

The program has been gradually expanded, and can now perform various other functions. None of these will break pairing, if the input is paired.

Quality trimming (either or both ends)
Quality filtering
Fixed-length trimming
Generation of histograms (base composition, quality, etc)
Subsampling (to a fraction of input reads, or an exact number of reads or bases)
Changing fasta line-wrapping length
Reverse-complementing (all reads or only read 2)
Adding /1 and /2 suffix to read names
GC-content filtering
Length-filtering
Testing for corrupted interleaved files

Reformat is compatible with any platform that supports Java 1.7 or higher. It also has a bash shellscript for simpler invocation. Typical usage examples:

Reformat fastq into fasta:
reformat.sh in=x.fq out=y.fa

Interleave paired reads:
reformat.sh in1=x1.fq in2=x2.fq out=y.fq

Note - you can actually use a shortcut if paired read files have the same name with a 1 and a 2. This is equivalent to the above command:
reformat.sh in=x#.fq out=y.fq

De-interleave reads:
reformat.sh in=x.fq out1=y1.fq out2=y2.fq

Verify that interleaving appears correct, assuming Illumina namimg conventions:
reformat.sh in=x.fq vint

Convert ASCII-33 to ASCII-64:
reformat.sh in=x.fq out=y.fq qin=33 qout=64

Quality-trim paired reads to Q10 on the left and right ends and discard reads shorter than 50bp after trimming:
reformat.sh in1=x1.fq in2=x2.fq out1=y1.fq out2=y2.fq outsingle=singletons.fq qtrim=rl trimq=10 minlength=50

Subsample 10% of the first 20000 pairs in an interleaved file:
reformat.sh in=x.fq out=y.fq reads=20000 samplerate=0.1 int=t
(in this case "int=t" overrides interleaving autodetection, to ensure reads are treated as pairs)

Pipe in a gzipped sam file and pipe out fasta:
reformat.sh in=stdin.sam.gz out=stdout.fa

Reverse-complement reads:
reformat.sh in=x.fq out=y.fq rcomp

For reformatting a file with very long sequences, Reformat will need more memory; just add the additional flag "-Xmx2g". For example, to change the line-wrapping length on the human genome (which has individual sequences over 200Mbp long) to 70 characters:
reformat.sh -Xmx2g in=HG19.fa.gz out=HG19_wrapped.fa.gz fastawrap=70

For additional functions, please run the shellscript with no arguments, or just read it with a text editor. If you have any questions, please post them in this thread.

For people using a non-bash terminal, you may need to type "bash reformat.sh" instead of just "reformat.sh".
For users of Windows or other platforms that do not support bash shellscripts, replace "reformat.sh" with "java -ea -Xmx200m /path/to/bbmap/current/ jgi.ReformatReads"
for example,
java -ea -Xmx200m C:\bbmap\current\ jgi.ReformatReads in=x.fq out=y.fa

Reformat can be downloaded with BBTools here:
https://sourceforge.net/projects/bbmap/

Projects opening at NBAGR

Wed, 24 Aug 2016 04:13:13 -0500

ICAR - NATIONAL BUREAU OF ANIMAL GENETIC RESOURCES

Karnal -132001 (Haryana)

A walk-in-Interview is proposed to be held at National Bureau of Animal Genetic Resources, Karnal (Haryana)-132001 at 10:30 AM on 05.09.2016 for the selection of Three Research Associate & One Young Professional - II as per details given below:

Name of the Scheme / Project: Center for Agricultural Bioinformatics. The post duration is Upto 31.032017 or earlier & Co-terminus with the project.

Research Associate (Three posts)

Date & Time of Interview: 10.30 A.M. on 05.09.2016

Essential Qualifications: PhD degree in any one of discipline/Subject Biotechnology/ Animal Genetics and Breeding/ Biochemistry/ Bioinformatics/Molecular Genetics OR Master’s degree in any one of above mentioned discipline/Subject with 4 years/5 years of Bachelor’s degree having 1st division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from Fellowship/Associateship

Desirable Qualifications: Experience in Database/Next Generation Sequencing Data analysis for 02 RA posts or working experience in molecular biology, gene expression data analysis, SNP genotyping and sequence data analysis, functional gene characterization for 01 RA post.

Young Professionals II One position

Date & Time of Interview: 10.30 A.M. on 05.09.2016

Essential: B. Tech or M.Tech. in Bioinformatics / Computer Science / Computer Application.

Desirable: Experience in Linux, MySQL, Java, C++/ PHP/ PERL R based data analysis and application development in Bioinformatics.

More Info : http://14.139.252.116/ADvertisementforCabinScheme.pdf

SRF/ Project Assistant Bioinformatics at NIRRH

Sun, 19 Jun 2016 09:11:13 -0500

SRF/ Project Assistant Bioinformatics recruitment in National Institute for Research in Reproductive Health (NIRRH)

Title of Project : 1. “Analysis Of The Structures Of Known Antimicrobial Peptides Using Machine Learning Algoitms And Molecular Dynamics Simulations”

Senior Research Fellow /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience and CSIR/UGC/ICMR net qualified OR First class M.Sc. in Bioinformatics/ Biological Sciences from recognized university with 2 years research experience Research experience in bioinformatics and wetlab methods.

Age: Not exceeding 35 Years

Pay Scale : Rs.18,000/- + 30% HRA Rs.14,000/- + 30% HRA

Project Assistant (Level-II) /1 Post

Qualification: First class M.Sc. in Bioinformatics/ Biological Sciences/Computer Sciences Training experience in bioinformatics and wetlab methods .

Age: Not exceeding 28 Years

Pay Scale : Rs.8,000
How to apply
Candidates must bring along with them all the relevant documents in original and one set of attested photocopies of the same and one passport size recent colour photograph.

Walk-in-Interview on 28.06.2016 between 09:00 hrs. to 12:00 hrs.

More at http://www.nirrh.res.in/links/job_oppotunities.htm

Samtools Primer !!

Jit — Thu, 23 Jun 2016 07:18:17 -0500

SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.

keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introduction
Revisions

    1.0: May 30, 2013: First public release on biobits.org.
    1.1: July 24, 2013: Updated with Disqus Comments / Feedback section.
    1.2: December 19, 2014: Multiple updates, including:
        Updated to use samtools 1.1 and bcftools 1.2.
        Updated usage for bcftools.

About

SAMtools is a popular open-source tool used in next-generation sequence analysis. This primer provides an introduction to SAMtools, and is geared towards those new to next-generation sequence analysis. The primer is also designed to be self-contained and hands-on, meaning that you only need to install SAMtools, and no other tools, and sample data sets are provided. Terms in bold are also explained in the glossary at the end of the document.

Address of the bookmark: http://biobits.org/samtools_primer.html

Kraken: ultrafast metagenomic sequence classification using exact alignments

Jit — Mon, 27 Jun 2016 11:01:44 -0500

Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/.

Krona

https://sourceforge.net/p/krona/home/krona/

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813/

NIPGR Hires Research Associate, JRF, Laboratory Assistant

Mon, 04 Jul 2016 20:12:14 -0500

National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg - Delhi, Delhi
₹15,000 a month
National Institute of Plant Genome Research (NIPGR) invites applications to recruit on vacant posts of Research Associate (RA), Junior Research Fellow (JRF) and Laboratory Assistant. Applications against these Sarkari Naukri can be submitted on or before 16 July 2016.
NIPGR Vacancy 2016 Details
1. Research Associate (RA)
Qualification: Ph.D. degree (awarded) in Molecular Biology/Biotechnolgy/Biochemistry/Plant Science/ Life Sciences/Bioinformatics or related field with 03 years post-doctoral research experience or 02 research papers in the journals of International repute are eligible to apply. Experience in the area of functional genomics, proteomics, metabolomics, multiomics and system biology will be preferred.
Age Limit: As Per Rules
2. Junior Research Fellow (JRF)
Qualification: M.Sc. degree or equivalent in Biotechnolgy/Biochemistry/Plant Science or Botany/ Life Sciences/Bioinformatics/ Molecular Biology or any other related field. Experience in advanced multiomics, big data analysis, molecular and system biology techniques will be given preference.
Age Limit: As Per Rules
3. Laboratory Assistant
Qualification: B.Sc. degree with 05 years working experience in government R&D Laboratory assisting in the field of molecular biology and genomis.
Pay Scale: Rs.15000/- Per Month
Age Limit: As Per Rules
How to Apply : Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Dr. Subhra Chakraborty, Staff Scientist-VII, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box NO. 10531, New Delhi – 110067 . The Last Date to submit application is 16 July 2016

Source: http://www.nipgr.res.in/careers/vacancies_latest.php#
Form at http://www.nipgr.res.in/files/careers/format_RA_JRF_LA.doc

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

RA Bioinformatics at National Bureau of Fish Genetic Resources

Mon, 25 Jul 2016 03:14:06 -0500

F.No. 1(16)/2016-Admn. (DBT-BBSRC Project)
Research Associate /JRF Biotechnology Job vacancies in National Bureau of Fish Genetic Resources on contract basis

Research Associate /01 Post

Essential: Ph.D. in Bioinformatics or 03 years research experience after Post Graduation in Bioinformatics with at least one research paper in Science Citation Indexed (SCI) journals.

Desirable: The candidate should have at least 1st Division during Graduation and Post Graduation. Experience in assembly/ analysis/ annotation of genomic/transcriptomic data generated on next generation sequencing platforms and working knowledge on different genomic softwares. Publications in Relevant Field.

Pay Scale : Rs. 36,000/- +20% HRA

Age: 40 years for male and 45 years for female candidates, as on the date of interview

Junior Research Fellow/ 01

Essential: Master Degree in Biotechnology/Life Science with Specialization in Molecular Biology with NET qualification.

Desirable: Research Experience in Molecular Biology. 1st Division during Graduation as well as Post Graduation. Publications in Relevant Field.

Pay Scale: Rs. 25,000/-+ 20% HRA for 1st and 2nd year and Rs. 28,000/-+ 20% HRA for 3rd year

Age: 35 years for male and 40 years for female candidates, as on the date of interview.
How to apply
A walk-in-interview will be held on 26.07.2016 at 10:00 hrs. at ICAR-National Bureau of Fish Genetic Resources, Lucknow.

More at http://www.nbfgr.res.in/Recruitments.aspx

SOAP2 : Short Oligonucleotide Analysis Package 2

Poonam Mahapatra — Wed, 23 May 2018 10:09:22 -0500

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Address of the bookmark: http://soap.genomics.org.cn/soapaligner.html

EMBOSS Apps

Jit — Wed, 27 Jul 2016 06:00:41 -0500

The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

Applications in the current release

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/