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ALPACA/PANGAIA ANNUAL WORKSHOP - Hackathon

Sequence to graph aligner evaluation

Aligners

vg Align - pass

Relevant links:

GraphAligner Align - pass

Relevant links:

minigraph Align - pass

Relevant links:

GraphChainer Align - pass

Relevant links:

minichain Align - pass

Relevant links:

PanAligner Align - pass

Relevant links:

PaSGAL Align - investigation

Reasons for investigation:

  • Output format is not canonical gaf/gam, investigation is needed to see if a conversion is feasible

Relevant links:

V-Align Align - investigation

Reasons for investigation:

  • The instructions are not clear
  • It may have everything it needs to run it
  • It is not clear what are inputs and outputs formats

Relevant links:

Vargas Align - fail

Reasons for failure:

  • It needs a specific graph format as input, that must be constructed with vargas define
  • It is not possible to convert gfa/vg to such format
  • It is thus impossible to fairly compare with other methods

Relevant links:

HGA Align - fail

Reasons for failure:

  • It need its proprietary input format, for which the only "documentation" is in RapidsAtHKUST/hga#1
  • It is not possible to convert gfa/vg to such format
  • The output format is not specified, and it is currently impossible to run the tool
  • It is thus impossible to fairly compare with other methods

Relevant links:

ASTARIX2 Align - fail

  • The output format is a TSV and doesn't have a gaf/gam conversion.
  • It may be possible to have a conversion tool, but the task is not trivial and the authors are not progressing on it, see eth-sri/astarix#3

Relevant links:

SeGram Align - fail

Reasons for failure:

  • There is no implementation of CLI
  • Using the tool requires manual changes to the source code to use desired input
  • An initial seed for the alignment is required to be specified manual
  • The output format is not specified, and it is currently impossible to run the tool
  • It is thus impossible to fairly compare with other methods

Relevant links:

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