BOL: All Site Activity

All Site Activity

- Rahul Nayak@rahul
Rahul Nayak created a new bio-script Estimate Genome Size 2468 days ago
Comments
- Abhimanyu Singh@abhimanyu
  
  Abhimanyu Singh 2101 days ago
  # count k-mers (see jellyfish documentation for options)
  gzip -dc reads1.fastq.gz reads2.fastq.gz | jellyfish count -m 31 -o fastq.counts -C -s 10000000000 -U 500 -t 30 /dev/fd/0
  # generate a histogram
  jellyfish histo fastq.counts_0 > fastq.counts_0.histo
  # generate a pdf graph of the histogram
  jellyplot.pl fastq.counts_0.histo
  # look at fastq.counts_0.histo.pdf and identify the approximate peak
  # use find_valleys.pl to help pinpoint the actual peak
  find_valleys.pl fastq.counts_0.histo
  # estimate the size and coverage
  estimate_genome_size.pl --kmer=31 --peak=42 --fastq=reads1.fastq.gz reads2.fastq.gz
- Jit@jit.aber
Jit bookmarked ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data 2471 days ago

ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and...

http://etetoolkit.org
- Jit@jit.aber
Jit posted to the wire 2474 days ago

Harness PacBio reads with assemblers https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Large-Genome-Assembly-with-PacBio-Long-Reads #Reads #Assemblers #PacBio
- Surabhi Chaudhary@surabhi
Surabhi Chaudhary published a blog post BBTools for bioinformatician ! 2474 days ago

BBTools can do almost everything now !
Comments
- Abhi@abhinav
  
  Abhi 1121 days ago
  Latest download link at https://sourceforge.net/projects/bbmap/files/BBMap_38.94.tar.gz
  More at https://sourceforge.net/projects/bbmap/files/
- Jit@jit.aber
Jit bookmarked Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive... 2474 days ago

Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the...

https://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/tallymer.html
- Jit@jit.aber
Jit posted to the wire 2474 days ago

Estimate the genome size https://bioinformatics.uconn.edu/genome-size-estimation-tutorial/ #Genome #Size #Estimate
- Muhammad Waseem@muhammadawan
Muhammad Waseem is now a friend with Jitendra Narayan 2475 days ago
Muhammad Waseem@muhammadawan
Jitendra Narayan@admin
- Jitendra Narayan@admin
Jitendra Narayan is now a friend with Muhammad Waseem 2475 days ago
Jitendra Narayan@admin
Muhammad Waseem@muhammadawan
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked MeDuSa: a multi-draft based scaffolder 2476 days ago

MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...

https://github.com/combogenomics/medusa
- Radha Agarkar@radhaagarkar
Radha Agarkar asked How to Plot a circular overlapping plots in Circos ? 2477 days ago

How to Plot a circular overlapping plots, as shown in pic. ? https://cloud.githubusercontent.com/assets/90373/13977453/0ba63268-f0ef-11e5-9b1b-6b0aa587e3ac.jpg I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/ data C D A...
- Radha Agarkar@radhaagarkar
Radha Agarkar is now a friend with BioStar 2477 days ago
Radha Agarkar@radhaagarkar
BioStar@biostar
- BioStar@biostar
BioStar is now a friend with Radha Agarkar 2477 days ago
BioStar@biostar
Radha Agarkar@radhaagarkar
- Jit@jit.aber
Jit bookmarked circosJS: d3 library to build circular graphs 2477 days ago

Circos is a javascript library to easily build interactive graphs in a circular layout. It's based on d3.js. It aims to be a javascript version of the Circos software. You should consider using Circos to show: relationships...

https://github.com/nicgirault/circosJS
- biogeek@biogeek
biogeek posted a new ad in the Opportunity Bioinformatics postdoctoral position at inStem 2477 days ago
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh created a page Computational resources for TE discovery and TE detection 2477 days ago

Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following...
- Jit@jit.aber
Jit posted to the wire 2478 days ago

#GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa
- Jit@jit.aber
Jit posted a new ad in the ResearchLabs The Brent Lab 2480 days ago
- Jit@jit.aber
Jit bookmarked Circoletto: visualizing sequence similarity with Circos 2480 days ago

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results. Online version and downloadable software package for offline use (source code in...

http://tools.bat.infspire.org/circoletto/
- Jit@jit.aber
Jit bookmarked GenomeTools: The versatile open source genome analysis software 2482 days ago

The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...

http://genometools.org/
- Jit@jit.aber
Jit bookmarked HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution 2482 days ago

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...

https://github.com/HingeAssembler/HINGE

BOL

Our Sponsors

All Site Activity