Kraken2 Alternatives

kraken2 reviews and mentions

• NHI Genome Studies: Mexico Govt Sept 12 Congressional hearing
  4 projects | /r/genetics | 14 Sep 2023

  3) Use Kraken2 to classify remaining reads. I'd start with the standard database.

• Refseq bacterial genomes to clean reads?
  1 project | /r/bioinformatics | 16 Feb 2023

  See more information in: kraken2 manual

• Fastest way to check E. coli contamination levels in eukaryotic NGS libraries?
  2 projects | /r/bioinformatics | 9 Feb 2023

  If you've got a fast solid state drive with >200G of space, then kraken2 + bracken works really well. First, use kraken2 to map reads to taxa in memory-mapped mode (to reduce system memory consumption):

• Inferring bacterial population sizes from metagenomic data
  1 project | /r/bioinformatics | 31 May 2022

  Yes, that can be done. Bacterial proportions is pretty much what programs like Kraken2 and Centrifuge do.

• Command line tool for species identification from Fasta files
  1 project | /r/bioinformatics | 11 Apr 2022

  Or Kraken2

• How can I generate a list of short (75-150bp) sequences from a bacterial genome and find out if any of those sequences are unique to that organism?
  1 project | /r/bioinformatics | 1 Jul 2021

  For bacterial metagenomic stuff you can quickly reduce the amount of sequences you need to BLAST by using Kraken2.

• Show HN: An API for running computationally intensive tools
  1 project | news.ycombinator.com | 9 Jun 2021

  While implementing and scaling data analysis pipelines at a biotech startup, I spent most of my time getting new tools running efficiently and scaling them. Implementing something like Kraken2 for genomic analysis (https://github.com/DerrickWood/kraken2) on our infrastructure took weeks and was hard to scale. I expected a library for running these tools on managed infrastructure via an API to exist – like Twilio for sending text messages or Stripe for processing payments – but I couldn't find any.

  Toolchest is an API for running data analysis tools easily (i.e. copy and paste a few lines of code), without managing the infrastructure. We're starting with computational genomics tools, but tools in other spaces can be added. Please drop me a message if you have a use case in mind! For example, I've thought about making hashcat powered by Tesla V100 GPUs accessible via our API.

  All feedback is welcome! If you're curious about how it works, feel free to check out our docs: https://toolchest-python-client.readthedocs.io/en/latest/use...

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  www.influxdata.com | 2 May 2024

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