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Profiler: MetaMaps #70

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sofstam opened this issue Apr 26, 2022 · 2 comments
Closed

Profiler: MetaMaps #70

sofstam opened this issue Apr 26, 2022 · 2 comments
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@sofstam
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enhancement Improvement for existing functionality needs-upstream-fix requires-module Profilers that do not yet have a nf-core/module WIP Work in progress
Milestone
1.3.0 - Crazy Corgi

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@sofstam
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sofstam commented Apr 26, 2022

Description of feature

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets. It simultaenously carries out read assignment and sample composition estimation.It is faster than classical exact alignment-based approaches, and its output is more information-rich than that of kmer-spectra-based methods. For example, each MetaMaps alignment comes with an approximate alignment location, an estimated alignment identity and a mapping quality.
The approximate mapping algorithm employed by MetaMaps is based on MashMap. MetaMaps adds a mapping quality model and EM-based estimation of sample composition.

https://www.nature.com/articles/s41467-019-10934-2

Work in progress in nf-core/modules:
MetaMaps
@sofstam sofstam added enhancement Improvement for existing functionality WIP Work in progress requires-module Profilers that do not yet have a nf-core/module first-release Functionality defined in initial design labels Apr 26, 2022
@jfy133 jfy133 added this to the First Release milestone May 1, 2022
@jfy133 jfy133 removed the first-release Functionality defined in initial design label May 19, 2022
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jfy133 commented May 19, 2022

Waiting for a bug fix from the developer, will bump to next release

@jfy133 jfy133 removed this from the First Release milestone Jun 2, 2022
@sofstam sofstam self-assigned this Mar 15, 2024
@sofstam sofstam added this to the 1.2.0 - Bouncy Basenji milestone Mar 15, 2024
@sofstam sofstam mentioned this issue Jun 13, 2024
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jfy133 commented Oct 22, 2024

There were still lots of problems on this despite a huge amount of work from @sofstam so I think this will not be worth it for the time being unless there are some updates to the tool

@jfy133 jfy133 closed this as completed Oct 22, 2024
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Labels
enhancement Improvement for existing functionality needs-upstream-fix requires-module Profilers that do not yet have a nf-core/module WIP Work in progress
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Hackathon: May 2024
Status: No status
Milestone
1.3.0 - Crazy Corgi
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@jfy133 @sofstam