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bcgsc
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tigmint
⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
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Add option to use ntLink for mapping step
#110
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lcoombe
closed
1 year ago
lcoombe
commented
1 year ago
When
mapping=ntLink
is added to the
tigmint-make
command, use ntLink for mapping long reads to the draft assembly instead of minimap2
For this ntLink mapping approach, doesn't split the long reads into pseudo-linked reads
Add option to use
memusg
for benchmarking the pipeline (if found in PATH)
Bugfix in
tigmint-cut
Could lead to distinct molecule extents being recognized as duplicates erroneously (More common to be seen when using ntLink mappings vs. minimap2)
mapping=ntLink
is added to thetigmint-make
command, use ntLink for mapping long reads to the draft assembly instead of minimap2memusg
for benchmarking the pipeline (if found in PATH)tigmint-cut