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make contig names unique when concatenating #44

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MarieLataretu opened this issue Nov 18, 2021 · 2 comments
Closed

make contig names unique when concatenating #44

MarieLataretu opened this issue Nov 18, 2021 · 2 comments
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@MarieLataretu

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@MarieLataretu
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problems at samtools

minimap2 seems to have no problems
@MarieLataretu MarieLataretu self-assigned this Nov 18, 2021
@matthuska
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This could be done by piping the fastq file through seqkit rename[1], which will append numbers to any sequences with duplicate names and leave the rest alone. The only challenge is finding a singularity container with seqkit.

[1] https://bioinf.shenwei.me/seqkit/usage/#rename

@MarieLataretu
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closed with #81

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@matthuska @MarieLataretu