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Latest activity

• • Jit@jit.aber

  

  Jit bookmarked CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) 1695 days ago

  Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...

  https://github.com/dutilh/CAT
• • Rahul Nayak@rahul

  

  Rahul Nayak answered the question When to use bbmap ? 1695 days ago

  BBMap is a global aligner and does not do any clipping by default and allows low-identity alignments. With the -slow flag, it will allow even more mismatches. Also, if you are mapping to genomic sequence (containing introns) then you need a...
• • biogeek@biogeek

  

  biogeek asked When to use bbmap ? 1695 days ago

  I recently came across bbmap. When to use it ?
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked GRIDSS: the Genomic Rearrangement IDentification Software Suite 1696 days ago

  GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants...

  https://github.com/PapenfussLab/gridss
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output 1699 days ago

  gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command...

  https://github.com/kammoji/gapFinisher
• • Rahul Nayak@rahul

  

  Rahul Nayak bookmarked LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly 1699 days ago

  LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...

  https://github.com/CAFS-bioinformatics/LR_Gapcloser
• • Jit@jit.aber

  

  Jit created a new bio-script Installing Busco version 4.0.6 1700 days ago
• • Radha Agarkar@radhaagarkar

  

  Radha Agarkar bookmarked Filtlong: quality filtering tool for long reads 1700 days ago

  Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...

  https://github.com/rrwick/Filtlong
• • Neel@neelam

  

  Neel posted to the wire 1700 days ago

  Learn Perl6 https://learnxinyminutes.com/docs/perl6/ #perl6 #Raku
• • Jit@jit.aber

  

  Jit posted to the wire 1702 days ago

  Ten Simple Rules for a successful remote postdoc https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007809 #PostDoc #Remote
• • Neel@neelam

  

  Neel commented on a bookmark List of Bioinformatics Vacancy, Jobs, Opportunity websites 1703 days ago

  Bioinformatics jobs in Africa https://www.mncjobs.co.za/search-jobs/bioinformatics
• • biogeek@biogeek

  

  biogeek commented on a bookmark Coronavirus Resources ! 1706 days ago

  Genome detective https://www.genomedetective.com/app/typingtool/virus/
• • Jit@jit.aber

  

  Jit commented on a bookmark Coronavirus Resources ! 1706 days ago

  SARS-CoV-2 SNP Calling pipeline https://github.com/DamienFr/CoV-homoplasy
• • Jit@jit.aber

  

  Jit commented on a bookmark Coronavirus Resources ! 1706 days ago

  UK Covid consortium https://www.cogconsortium.uk/data/
• • Jit@jit.aber

  

  Jit commented on a bookmark Coronavirus Resources ! 1706 days ago

  CoViD Selection analysis http://virological.org/t/selection-analysis-of-gisaid-sars-cov-2-data/448
• • Jit@jit.aber

  

  Jit commented on a bookmark Coronavirus Resources ! 1706 days ago

  UK resource in CoViD19 http://cov-glue.cvr.gla.ac.uk/#/home https://macman123.shinyapps.io/ugi-scov2-alignment-screen/
• • Jit@jit.aber

  

  Jit commented on the blog Important Journals, Blogs and Forums for Bioinformaticians 1708 days ago

  Molecular informatics journal is also a good alternative for bioinformatics tools publication https://onlinelibrary.wiley.com/toc/18681751/2020/39/4
• • Jit@jit.aber

  

  Jit bookmarked Synteny and Rearrangement Identifier (SyRI) 1708 days ago

  SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI...

  https://schneebergerlab.github.io/syri/
• • Jit@jit.aber

  

  Jit bookmarked NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences 1708 days ago

  NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly...

  https://github.com/uio-cels/NucDiff
• • Shruti Paniwala@shruti

  

  Shruti Paniwala created a new bio-script Install kraken on linux 1709 days ago

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