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OpenGene / fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.
MIT License
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multiple fastv html or json reports view #12

Open intikhab opened 3 years ago

intikhab commented 3 years ago

Dear FastV Team,

I am testing fastv for many samples related to a reference virus genome. Is it possible to combine resulting html files for a comparative view?

This feature would be very useful if available.

Many Thanks,

IA

sfchen commented 3 years ago

This isn't a common requirement, so it won't be implemented immediately.

Probably you can visualize the results using Python or other programming scripts to parse the JSON outputs.

intikhab commented 3 years ago

Dear Shifu,

I had a related question on point 4 of fastv:

fastv accepts FASTQ files as input, and then:

  1. performs data QC and quality filtering as fastp does (cut adapters, remove low quality reads, correct wrong bases).
  2. scans the clean data to collect the sequences that containing any unique k-mer, or can be mapped to any reference microbial genomes.
  3. makes statistics, visualizes the result in HTML format, and output the results in JSON format.
  4. outputs the on-target sequencing reads so that they can be analyzed by downstream tools.

When using viruses as the database, it seems we are not able to save on target reads, mentioned in point 4 above, using option:

-c viral.kc.fasta.gz

Can you please help?

Thanks,

IA ?

-- Intikhab Alam, PhD

Research Scientist Computational Bioscience Research Centre (CBRC), Building #3, Office #4328 4700 King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900, KSA W: http://www.kaust.edu.sahttps://webmail.kaust.edu.sa/owa/redir.aspx?C=wkduJ0ChSE-OkyUQwL9vutDH6L5Gg9EImiJ7GyYOxcPLuActd9iwo85DHDgQZup2zR1MyXCk7as.&URL=http%3a%2f%2fwww.kaust.edu.sa T +966 (0) 2 808-2423 F +966 (2) 802 0127

From: Shifu Chen notifications@github.com Sent: 29 December 2020 08:57 To: OpenGene/fastv Cc: Intikhab S. Alam; Author Subject: Re: [OpenGene/fastv] multiple fastv html or json reports view (#12)

This isn't a common requirement, so it won't be implemented immediately.

Probably you can visualize the results using Python or other programming scripts to parse the JSON outputs.

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