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• • Jit@jit.aber

  

  Jit bookmarked VG: variation graph data structures, interchange formats, alignment, genotyping, and variant... 2419 days ago

  Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...

  https://github.com/vgteam/vg
• • Jit@jit.aber

  

  Jit posted to the wire 2419 days ago

  NGS alignment and variant calling tutorial https://github.com/ekg/alignment-and-variant-calling-tutorial #NGS #variant #snp #tools #tutorial #calling
• • Jit@jit.aber

  

  Jit bookmarked vt: a variant tool set that discovers short variants from Next Generation Sequencing data. 2419 days ago

  vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt

  https://genome.sph.umich.edu/wiki/Vt
• • Jit@jit.aber

  

  Jit bookmarked MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants 2419 days ago

  MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being...

  https://github.com/AlgoLab/malva
• • Jit@jit.aber

  

  Jit bookmarked Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search 2419 days ago

  Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn...

  https://github.com/redayounsi/2KP2P
• • Jit@jit.aber

  

  Jit bookmarked FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads 2419 days ago

  FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...

  http://bioinfo.ut.ee/FastGT/
• • Jit@jit.aber

  

  Jit bookmarked Kevler: Reference-free variant discovery in large eukaryotic genomes 2419 days ago

  Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...

  https://github.com/kevlar-dev/kevlar
• • Jit@jit.aber

  

  Jit posted to the wire 2419 days ago

  Explore the DNA with deep learning ! https://blog.floydhub.com/exploring-dna-with-deep-learning/ #Learn #DNA #Deep #Learning #AI #Machine
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a bookmark Genome in a Bottle (GIAB) Consortium 2420 days ago

  Benchmark (or "High-confidence") variant calls and regions:We developed an integration pipeline to utilize sequencing data generated by multiple technologies to generate variant calls and regions for use in benchmarking and validating variant...
• • Rahul Nayak@rahul

  

  Rahul Nayak commented on a bookmark Genome in a Bottle (GIAB) Consortium 2420 days ago

  GitHub https://github.com/genome-in-a-bottle
• • Jit@jit.aber

  

  Jit posted to the wire 2420 days ago

  The future of the postdoc https://www.nature.com/news/the-future-of-the-postdoc-1.17253 #Future #PostDoc #Job #Idea #discussion
• • Jit@jit.aber

  

  Jit posted to the wire 2420 days ago

  Core services: Reward bioinformaticians https://www.nature.com/news/core-services-reward-bioinformaticians-1.17251 #Service #Core #Reward #Bioinformatician
• • Jit@jit.aber

  

  Jit is now a friend with Pijush 2420 days ago

  • Jit@jit.aber

  

  • Pijush@topijush

  
• • Pijush@topijush

  

  Pijush is now a friend with Jit 2420 days ago

  • Pijush@topijush

  

  • Jit@jit.aber

  
• • Jitendra Narayan@admin

  

  Jitendra Narayan is now a friend with Pijush 2420 days ago

  • Jitendra Narayan@admin

  

  • Pijush@topijush

  
• • Pijush@topijush

  

  Pijush is now a friend with Jitendra Narayan 2420 days ago

  • Pijush@topijush

  

  • Jitendra Narayan@admin

  
• • Rahul Nayak@rahul

  

  Rahul Nayak created a new bio-script Perl script to remove duplicated lines ! 2420 days ago
• • Jit@jit.aber

  

  Jit commented on a bookmark Genome in a Bottle (GIAB) Consortium 2420 days ago

  Some useful links for GIAB ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/ https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA200694&o=acc_s%3Aa https://jimb.stanford.edu/giab-resources
• • Rahul Agarwal@raag

  

  Rahul Agarwal posted to the wire 2422 days ago

  2020 NGBT_https://www.sgrfconferences.org/2020/NGBT/ #genomics #conference #india
• • Rahul Agarwal@raag

  

  Rahul Agarwal posted to the wire 2422 days ago

  https://www.biorxiv.org/content/10.1101/2020.01.22.914952v2.full.pdf+html #coronavirus #bat #genome

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