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• • Jit@jit.aber

  

  Jit bookmarked SeqMonk:A tool to visualise and analyse high throughput mapped sequence data 2314 days ago

  SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic...

  http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
• • BioStar@biostar

  

  BioStar bookmarked STRUM: structure-based prediction of protein stability changes upon single-point mutation 2315 days ago

  STRUM is a method for predicting the fold stability change (ΔΔG) of protein molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy changes on a variety of features...

  https://zhanglab.ccmb.med.umich.edu/STRUM/
• • Jit@jit.aber

  

  Jit bookmarked Ensembl Variation - Calculated variant consequences 2315 days ago

  For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the variant may have on each transcript. The set of consequence...

  https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html
• • BioStar@biostar

  

  BioStar posted to the wire 2315 days ago

  https://github.com/Ensembl/ensembl-vep #Variant #Effect #Predictor #Github
• • BioStar@biostar

  

  BioStar posted to the wire 2315 days ago

  Variant Effect Predictor http://www.ensembl.org/Tools/VEP #Variant #Effect #Predictor
• • BioStar@biostar

  

  BioStar replied on the discussion topic Want to Know which genome assembler rule the world ? in the group Next Generation Sequencing (NGS) 2315 days ago

  Genome assembly tools at https://bioinformaticsonline.com/search?q=assembly&entity_type=object&entity_subtype=bookmarks&offset=0&search_type=entities
• • BioStar@biostar

  

  BioStar joined the group Next Generation Sequencing (NGS) 2315 days ago
• • BioStar@biostar

  

  BioStar created a new bio-script Perl script to extract a sequence from multifasta with range ! 2317 days ago
• • BioStar@biostar

  

  BioStar bookmarked P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads 2318 days ago

  P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...

  http://www.fishbrowser.org/software/P_RNA_scaffolder/#
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh posted to the wire 2318 days ago

  Efficiency of #PacBio long read #correction by 2nd generation #Illumina sequencing https://www.sciencedirect.com/science/article/pii/S0888754317301660
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked LSC: Improving PacBio Long Read Accuracy by Short Read Alignment 2318 days ago

  Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...

  https://www.healthcare.uiowa.edu/labs/au/LSC/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked LoRMA: A tool for correcting sequencing errors in long reads 2318 days ago

  An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...

  https://gite.lirmm.fr/lorma/lorma-releases/wikis/home
• • BioStar@biostar

  

  BioStar posted to the wire 2320 days ago

  #Nigerian Society for #Bioinformatics and Computational Biology (#NISBCB) http://cubre.covenantuniversity.edu.ng/index.php/nigeria-society-for-bioinformatics-and-computatational-biology-nisbcb/#.W4_7m
• • BioStar@biostar

  

  BioStar bookmarked DEPARTMENT OF GENETICS, GENOMICS AND BIOINFORMATICS, National Biotechnology Development Agency,... 2320 days ago

  The Genetics, Genomics & Bioinformatics Department (GBBD) at NABDA is unique, encompassing all facets of modern genetics and bioinformatics research. Trans-disciplinary research being conducted in our laboratories would lead to cures for human...

  http://www.nabda.gov.ng/departments/genetics-genomics-and-bioinformatics
• • BioStar@biostar

  

  BioStar posted to the wire 2320 days ago

  Bioinformatics in Nigeria http://bioinformatics.ui.edu.ng/ #Nigeria #Bioinformatics
• • BioStar@biostar

  

  BioStar posted to the wire 2320 days ago

  Computational Biology and Bioinformatics in Nigeria https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998874/ #Nigeria #Bioinformatics #Scope
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2320 days ago

  Multi-line fasta to single line fasta $ perl -pe '/^>/ ? print "\n" : chomp' in.fasta | tail -n +2 > out.fasta #Multiline #Singleline #Fasta
• • Rahul Nayak@rahul

  

  Rahul Nayak published a blog post Setting python version as default on Linux 2321 days ago

  If you have a later version than 2.6 you'll need to set 2.6 as the default Python.
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2321 days ago

  Snakemake install Ubuntu $ sudo apt-get install snakemake #snakemake #Ubuntu #Install
• • Jit@jit.aber

  

  Jit bookmarked Snakemake—a scalable bioinformatics workflow engine 2322 days ago

  Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. 

  https://bioconda.github.io/recipes/snakemake/README.html

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