<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31123?offset=990 https://bioinformaticsonline.com/blog/view/30874/important-journals-blogs-and-forums-for-bioinformaticians Wed, 08 Feb 2017 09:15:31 -0600 https://bioinformaticsonline.com/blog/view/30874/important-journals-blogs-and-forums-for-bioinformaticians <![CDATA[Important Journals, Blogs and Forums for Bioinformaticians]]> Journals. Most journals have RSS feeds for their current updates.

Blogs. Some of these blogs are very relevant to bioinfo jobs. Others are more personal interest.

  • Variance Explained: David Robinson’s blog (Data Scientist at Stack Overflow, works in R and Python).
  • Global Biodefense: News on pathogens, outbreaks, and preparedness, with periodic posts on genomics and bioinformatics-related developments and funding opportunities.
  • In between lines of code: Lex Nederbragt’s blog on biology, sequencing, bioinformatics, …
  • Simply Statistics: A statistics blog by Rafa Irizarry, Roger Peng, and Jeff Leek.
  • Bits of DNA: Reviews and commentary on computational biology by Lior Pachter (fair warning: dialogue here can get a bit heated!).
  • Blue Collar Bioinformatics: articles related tool validation and the open source bioinformatics community.
  • Microbiome Digest – Bik’s Picks: A daily digest of scientific microbiome papers, by Elisabeth Bik, Science Editor at uBiome.
  • Living in an Ivory Basement: Titus Brown’s blog on metagenomics, open science, testing, reproducibility, and programming.
  • Enseqlopedia: James Hadfield’s blog on all things NGS.
  • Epistasis Blog: Jason Moore’s computational biology blog.
  • RStudio Blog: announcements about new RStudio functionality, updates about the tidyverse, and more.
  • nextgenseek.com: Next-Gen Sequencing Blog covering new developments in NGS data & analysis.
  • RNA-Seq Blog: Transcriptome Research & Industry News.
  • The Allium: We all need a little humor in our lives. Like The Onion, but for science.

Forums.

]]> Jit https://bioinformaticsonline.com/opportunity/view/30928/jrf-bioinformatics-job-vacancies-in-tezpur-university Tue, 14 Feb 2017 16:40:26 -0600 <![CDATA[JRF Bioinformatics job vacancies in Tezpur University]]> Memo No. DoRD/CSE/SSS/20-295/112-A Date: 01/02/2017

Project Title : “Integrating genome scale metabolic analysis of model plant pathogen Ralstonia solanacearum with RNAseq and fluxomics”

Essential qualification : M.Tech. in CSE/IT (With specialization in Computational Biology/Bioinformatics) or M.Sc. in Bioinformatics/Biosciences/Molecular Biology Biotechnology preferably with NET/GATE/BET. Candidates should have minimum 55 % mark both in 10th and 10+2 Science examinations and mathematics at 10+2 Science. Desirable: Preference will be given to the candidates having experience in computational analysis of genome sequences or similar projects.

No. of Post : 01

Remuneration : Rs. 25,000/- for the 1st two years and Rs. 28,000/- for the 3rd year for SRF and applicable to the candidate having post graduate degree in Basic Science with NET/GATE/BET qualification or post graduate degree in professional course. Rs. 12,000/- for the 1st two years and Rs. 14,000/- for the 3 rd year for SRF,

Age : 28 years

Duration : Three (03) years or till completion of the project or until further order, whichever is earlier.

Hiring Process : Walk - In
Job Role: Research/JRF/SRF

Walk-in-interview will be held on 17th February, 2017, 11.15 a.m. at the office of the Head, Department of Computer Science and Engineering, Tezpur University.

Interested candidates may appear before the interview board with original documents from 10th standard onwards and photocopies of mark sheets, certificates, testimonials, caste certificate (if applicable), experience certificate certificates of NET/GATE/BET or similar examination qualifications, any other testimonials and a copy of recent curriculum vitae (CV) on the day of interview.

More at http://www.tezu.ernet.in/ProjectWalkin/Advt-DoRD-CSE-SSS-20-295-112-A.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/30976/brig Thu, 16 Feb 2017 13:14:25 -0600 https://bioinformaticsonline.com/bookmarks/view/30976/brig <![CDATA[BRIG]]> BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

  • Images show similarity between a central reference sequence and other sequences as concentric rings.
  • BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
  • Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
  • Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
  • BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

 

Address of the bookmark: http://brig.sourceforge.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31024/dagchainer-computing-chains-of-syntenic-genes-in-complete-genomes Fri, 17 Feb 2017 16:13:35 -0600 https://bioinformaticsonline.com/bookmarks/view/31024/dagchainer-computing-chains-of-syntenic-genes-in-complete-genomes <![CDATA[DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes]]> The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed.

This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.

Address of the bookmark: http://dagchainer.sourceforge.net/

]]> Abhimanyu Singh https://bioinformaticsonline.com/bookmarks/view/31089/conpade-genome-assembly-ploidy-estimation-from-next-generation-sequencing-data Fri, 24 Feb 2017 04:55:41 -0600 https://bioinformaticsonline.com/bookmarks/view/31089/conpade-genome-assembly-ploidy-estimation-from-next-generation-sequencing-data <![CDATA[ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data]]> ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. They also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. 

https://github.com/microsoftgenomics

Address of the bookmark: https://github.com/microsoftgenomics

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31139/pbsuite-software-for-long-read-sequencing-data-from-pacbio Mon, 27 Feb 2017 09:54:47 -0600 https://bioinformaticsonline.com/bookmarks/view/31139/pbsuite-software-for-long-read-sequencing-data-from-pacbio <![CDATA[PBSuite: Software for Long-Read Sequencing Data from PacBio]]> PBJelly - the genome upgrading tool. 
PBHoney - the structural variation discovery tool 

Both are contained within the PBSuite code found in downloads.

----- PBJelly -----
Read The Paper 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. 

----- PBHoney -----
Read The Paper
http://www.biomedcentral.com/1471-2105/15/180/abstract

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Address of the bookmark: https://sourceforge.net/projects/pb-jelly/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31295/mycc-accurate-binning-of-metagenomic-contigs-via-automated-clustering-sequences-using-information-of-genomic-signatures-and-marker-genes Fri, 03 Mar 2017 08:34:23 -0600 https://bioinformaticsonline.com/bookmarks/view/31295/mycc-accurate-binning-of-metagenomic-contigs-via-automated-clustering-sequences-using-information-of-genomic-signatures-and-marker-genes <![CDATA[MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes]]> MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments.

More at http://www.nature.com/articles/srep24175

Address of the bookmark: https://sourceforge.net/projects/sb2nhri/files/MyCC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31345/prokka-tool-for-the-rapid-annotation-of-prokaryotic-genomes Mon, 06 Mar 2017 03:49:57 -0600 https://bioinformaticsonline.com/bookmarks/view/31345/prokka-tool-for-the-rapid-annotation-of-prokaryotic-genomes <![CDATA[Prokka: tool for the rapid annotation of prokaryotic genomes]]> Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.

 

Address of the bookmark: http://www.vicbioinformatics.com/software.prokka.shtml

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31375/cocacola-binning-metagenomic-contigs-using-sequence-composition-read-coverage-co-alignment-and-paired-end-read-linkage Tue, 07 Mar 2017 08:50:57 -0600 https://bioinformaticsonline.com/bookmarks/view/31375/cocacola-binning-metagenomic-contigs-using-sequence-composition-read-coverage-co-alignment-and-paired-end-read-linkage <![CDATA[COCACOLA (binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge)]]> COCACOLA is a general framework that combines different types of information: sequence COmposition, CoverAge across multiple samples, CO-alignment to reference genomes and paired-end reads LinkAge to automatically bin contigs into OTUs. Furthermore, COCACOLA seamlessly embraces customized prior knowledge to facilitate binning accuracy.

News: Python version of COCACOLA is available now!

Address of the bookmark: https://github.com/younglululu/COCACOLA

]]> Jit https://bioinformaticsonline.com/view/459 Thu, 11 Jul 2013 14:39:19 -0500 https://bioinformaticsonline.com/view/459 <![CDATA[Python vs Perl]]> Why bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?

]]> Rahul Agarwal