seqan3

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[Infra] Python bindings

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Hi, are there python bindings for SeqAn3? I found bindings for an older version https://github.com/JohnReid/pyseqan but last release was in 2014.

BjornFJohansson

[MISC] FastQ performance

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Based on an external application that converts FastQ to FastA I have benchmarked and optimised the affected code. Depending on System this yields a 2x speed-up but the application is...

h-2

wip traceback alignment

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The draft PR for the traceback computation in the new alignment. solves seqan/product_backlog#74 ### Changes * Adds a trace matrix that stores the entire trace column * Adds a pairwise_alignment...

rrahn

[FEATURE] seqan3::align_multiple for MSA dependent on seqan2

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Part of https://github.com/seqan/product_backlog/issues/104 Note: Changing the result type as discussed into a `seqan3::multiple_sequence_alignment_result` type that models a range over aligned sequences will follow in a separate PR.

smehringer

Search outparam

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This is a possibly updated version of #1528 For more discussion see https://github.com/seqan/product_backlog/issues/29

h-2

NOT FOR MERGE @eseiler some inspiration for performance tuning of the search. This PR improves `unidirectional_search_all/highErrorReadsSearch0` by 20% (impact on complex searches is expectedly smaller). Left to do in this...

h-2

[Alignment] Meta-issue

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This is a meta-issue collecting tasks which are transformed into single issues: ~~The implementation is blocked by #295~~ # General `align` seems to be the best fit for the namespace...

rrahn

**Level 1 - Easy** Provide a `read_sequence_record` and `write_sequence_record` in the BAM format (very similar to `format_sam.hpp`).

rrahn

[Infra] Use SIMD Everywhere

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"SIMD Everywhere" is a MIT licensed header-only library that makes it easier to use SIMD instructions across CPU types. They have most, but not all, of the instructions used in...

mr-c

[DOC] doxygen 1.9.5/1.9.6

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eseiler