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- Rahul Agarwal@raag
Rahul Agarwal is now a friend with biogeek 2523 days ago
Rahul Agarwal@raag
biogeek@biogeek
- biogeek@biogeek
biogeek is now a friend with Rahul Agarwal 2523 days ago
biogeek@biogeek
Rahul Agarwal@raag
- Jit@jit.aber
Jit answered the question What are the difference between Synteny and Collinearity terms? 2524 days ago

These terms are interchangeably used in genomics. The major difference between synteny and collinearity is that synteny is (genetics|of multiple genes) the condition of being located on the same chromosome or region of genome while collinearity...
- Jit@jit.aber
Jit bookmarked 3d-dna: 3D de novo assembly (3D DNA) pipeline 2524 days ago

This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science, 2017. Unless otherwise...

https://github.com/theaidenlab/3d-dna
- Rahul Nayak@rahul
Rahul Nayak posted a new ad in the ResearchLabs ShendureLab 2524 days ago
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 2524 days ago

Bioinformatics tools collection and database https://bio.tools #tools #database #search #list
- Rahul Nayak@rahul
Rahul Nayak bookmarked Rectangle Graph for Repeat Resolution in Genome Assembly 2524 days ago

Ultimate tool for resolving repeats in genome assemblies. Though the specific implementation of the idea of the rectangle graph approach is already included into the current SPAdes distribution, we're also releasing the Rectangle Graph Module...

http://bioinf.spbau.ru/en/rectangles
- Rahul Nayak@rahul
Rahul Nayak asked What are the difference between Synteny and Collinearity terms? 2524 days ago

I sometime got confused with Synteny and Collinearity terminology. I am still wondering about the major differences.
- Rahul Nayak@rahul
Rahul Nayak bookmarked CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies 2524 days ago

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of...

https://cblab.org/camsa/
- Rahul Nayak@rahul
Rahul Nayak bookmarked xmatchview: smith-waterman alignment visualization 2524 days ago

xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and...

https://github.com/warrenlr/xmatchview
- biogeek@biogeek
biogeek published a blog post Bioinformatics tools developed for Oxford Nanopore data analysis ! 2524 days ago

One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly.
Comments
- Rahul Nayak@rahul
  
  Rahul Nayak 2457 days ago
  
  NanoComp: comparing multiple runs
  
  NanoStat: statistic summary report of reads or alignments
  
  NanoFilt: filtering and trimming of reads
  
  NanoLyse: removing contaminant reads (e.g. lambda control DNA) from fastq
- Rahul Nayak@rahul
  
  Rahul Nayak 1753 days ago
  Basic commands for genome assembly
  https://raw.githubusercontent.com/rrwick/Long-read-assembler-comparison/master/supplementary_figures/Fig_S04_commands.png
- biogeek@biogeek
biogeek bookmarked Ra assembler - a de novo DNA assembler for third generation sequencing data 2524 days ago

Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and Genome Institute of Singapore (GIS). Ra is in...

https://github.com/mariokostelac/ra-integrate/
- biogeek@biogeek
biogeek published a blog post List of cancer genomics research web resources ! 2524 days ago

Major web resources for cancer genomics research
- biogeek@biogeek
biogeek is now a friend with Jit 2524 days ago
biogeek@biogeek
Jit@jit.aber
- Jit@jit.aber
Jit is now a friend with biogeek 2524 days ago
Jit@jit.aber
biogeek@biogeek
- biogeek@biogeek
biogeek commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2524 days ago

Methods journals also accept bioinformatics papers https://www.journals.elsevier.com/methods
- Jit@jit.aber
Jit commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2524 days ago

Informative bioinformatics bloggers Diving into Genetics and Genomics YOKOFAKUN Getting Genetics Done Gigabase or gigabyte Genome Spot CoreGenomics The Genome Factory RajLab Omics! Omics! Next-Gen Sequencing Blasted...
- Jit@jit.aber
Jit commented on a page titled Virtual Bioinformatics Online Tutorial 2524 days ago

Bioinformatics online training resources Cancer Research UK Cambridge Bioinformatics core facility HarvardX Biomedical Data Science Open Online Training SIB Virtual Computational Biology Seminar Series Training Courses by the Babraham...
- Jit@jit.aber
Jit answered the question What are the best known workflow or tutorial for SNP calling? 2524 days ago

You should try following as well Genome-Wide Association Studies Variant Calling Pipeline: FastQ to Annotated SNPs in Hours A simple SNP calling pipeline Hands-on Tutorial on SNP Calling Genome Analysis Toolkit
- Jit@jit.aber
Jit answered the question What are the best packages to visualize the data in R ? 2524 days ago

I mostly use these R packages Circos Plot Introduction to Circos plot ppt RCircos: an R package for Circos 2D track plots Package RCircos OmicCircos Circos Google Group Network visualization with R Useful link circlize Useful link Useful...

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