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Latest activity

• • BioJoker@biojoker

  

  BioJoker posted a new ad in the Opportunity Research opening @ IBAB, Bengaluru 2174 days ago
• • Jit@jit.aber

  

  Jit posted to the wire 2174 days ago

  for i in $(ls *.ab1); do convert_trace -out_format scf < $i > ${i%.ab1*}.scf; done #Convert #AB12SCF #SCF #AB1
• • Neel@neelam

  

  Neel posted to the wire 2175 days ago

  (smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research 2176 days ago

  GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs....

  https://github.com/b-brankovics/grabb
• • Jit@jit.aber

  

  Jit bookmarked Genome assembly forensics: finding the elusive mis-assembly 2176 days ago

  We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...

  http://amos.sourceforge.net/wiki/index.php/AMOS
• • Rahul Nayak@rahul

  

  Rahul Nayak posted to the wire 2176 days ago

  A De Novo Genome #Assembly Algorithm for #Repeats and Nonrepeats https://www.hindawi.com/journals/bmri/2014/736473/
• • Neel@neelam

  

  Neel commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites 2178 days ago

  Biotechnology jobs in India http://www.dbtindia.nic.in/vacancies/
• • BioStar@biostar

  

  BioStar bookmarked NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads 2178 days ago

  NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file...

  https://github.com/rebeccaroisin/nxrepair
• • Jit@jit.aber

  

  Jit posted to the wire 2180 days ago

  Bioconda packages for bioinformatician https://conda-static.anaconda.org/bioconda/ #conda #bioconda #packages #list #tools
• • BioStar@biostar

  

  BioStar published a blog post List of tools frequently used while genome assembly 2180 days ago

  To decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655
• • Jit@jit.aber

  

  Jit bookmarked Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish... 2180 days ago

  Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...

  https://github.com/nanoporetech/katuali
• • Jit@jit.aber

  

  Jit commented on a bookmark Roary: the Pan Genome Pipeline 2180 days ago

  Tutorial at http://sepsis-omics.github.io/tutorials/modules/roary/
• • Jit@jit.aber

  

  Jit commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 2180 days ago

  Genomics, Proteomics & Bioinformatics https://www.journals.elsevier.com/genomics-proteomics-and-bioinformatics
• • Jit@jit.aber

  

  Jit bookmarked Roary: the Pan Genome Pipeline 2180 days ago

  Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of...

  https://sanger-pathogens.github.io/Roary/

  Comments

  • • Jit@jit.aber

    

    Jit 2180 days ago

    Tutorial at http://sepsis-omics.github.io/tutorials/modules/roary/
• • Abhimanyu Singh@abhimanyu

  

  Abhimanyu Singh bookmarked SvABA: Genome-wide detection of structural variants and indels by local assembly 2181 days ago

  SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....

  https://github.com/walaj/svaba
• • Jit@jit.aber

  

  Jit bookmarked HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene... 2181 days ago

  A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar...

  https://github.com/DittmarLab/HGTector
• • BioJoker@biojoker

  

  BioJoker bookmarked ClipCrop: a tool for detecting structural variations with single-base resolution using... 2182 days ago

  ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated...

  https://github.com/shinout/clipcrop
• • BioJoker@biojoker

  

  BioJoker bookmarked SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2182 days ago

  FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only...

  https://bioinf.shenwei.me/seqkit/usage/
• • BioJoker@biojoker

  

  BioJoker bookmarked Osprey: Network Visualization System 2182 days ago

  Osprey is a software platform for the visualization of complex biological interaction networks. Osprey builds data-rich graphical representations from Gene Ontology (GO) annotated interaction data maintained by the BioGRID. Osprey is...

  https://osprey.thebiogrid.org/
• • BioJoker@biojoker

  

  BioJoker bookmarked molinspiration: broad range of cheminformatics software tools supporting molecule manipulation 2182 days ago

  Molinspiration offers broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation,...

  https://www.molinspiration.com/

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