Issues

• Add longer reads to benchmark

  ksahlin/strobealign#660 · Filter by author ksahlin opened on Oct 15, 2026

• Reconsider how -f works and how the filter_cutoff is set

  ksahlin/strobealign#635 · Filter by author marcelm opened on Sep 16, 2026
  1

• Do not index N regions

  ksahlin/strobealign#602 · Filter by author marcelm opened on Jun 12, 2026

• Having two modes: short reads and long reads

  ksahlin/strobealign#599 · Filter by author ksahlin opened on Jun 11, 2026
  2

• Ideas for reducing memory usage

  ksahlin/strobealign#597 · Filter by author marcelm opened on Jun 10, 2026
  2

• SSW banded_sw heap-buffer-overflow due to uninitialized ref_begin1

  ksahlin/strobealign#568 · Filter by author parlar opened on Mar 5, 2026

• Use ISA-L even in the Rust version

  ksahlin/strobealign#561 · Filter by author marcelm opened on Feb 19, 2026
  3

• Experimental ancient DNA modifications

  ksahlin/strobealign#523 · Filter by author teepean opened on Oct 5, 2025
  6

• [Feature Request] - Optionally output unaligned reads as fastq

  ksahlin/strobealign#520 · Filter by author jolespin opened on Sep 22, 2025

• CLI option to always include SEQ/QUAL in SAM output

  ksahlin/strobealign#507 · Filter by author sjaenick opened on Jun 25, 2025
  2

• Release Python bindings to PyPI

  ksahlin/strobealign#496 · Filter by author althonos opened on Apr 27, 2025
  2

• Potential issues in using same reference length for large libraries of variable read length?

  ksahlin/strobealign#493 · Filter by author Rridley7 opened on Apr 8, 2025
  3

• Speed vs. reference size

  ksahlin/strobealign#484 · Filter by author shiraz-shah opened on Mar 12, 2025
  12

• Feature request: Keep index in memory while mapping multiple samples in a row

  ksahlin/strobealign#483 · Filter by author shiraz-shah opened on Mar 11, 2025
  1

• Some reads are almost entirely soft-clipped

  bug
  ksahlin/strobealign#477 · Filter by author marcelm opened on Jan 21, 2025
  6

• Investigating the scoring function in paired end mode

  ksahlin/strobealign#469 · Filter by author ksahlin opened on Dec 11, 2024

• Question about SyncmerIterator

  ksahlin/strobealign#463 · Filter by author drtconway opened on Dec 2, 2024
  4

• Question: Identity threshold

  ksahlin/strobealign#462 · Filter by author stas-malavin opened on Nov 26, 2024
  12

• estimating breadth of coverage with strobealign --aemb

  ksahlin/strobealign#456 · Filter by author wwood opened on Nov 12, 2024
  3

• Reconsider the has_shared_substring heuristic

  ksahlin/strobealign#437 · Filter by author marcelm opened on Sep 3, 2024

• Start indexing while still reading the reference

  ksahlin/strobealign#436 · Filter by author marcelm opened on Aug 22, 2024

• All secondary alignments lost

  ksahlin/strobealign#433 · Filter by author tprodanov opened on Aug 1, 2024
  7

• Do more hamming distance attempts?

  ksahlin/strobealign#419 · Filter by author ksahlin opened on Apr 24, 2024

• Support for both open and closed syncmers

  feature
  ksahlin/strobealign#417 · Filter by author ksahlin opened on Apr 19, 2024

• Lower bounding w_min to 1 instead of 0?

  ksahlin/strobealign#416 · Filter by author ksahlin opened on Apr 18, 2024
  1