Issues

• Unusual --version output

  maickrau/GraphAligner#117 · Filter by author tseemann opened on Apr 12, 2026

• Purpose of maxXScore and errorCost

  maickrau/GraphAligner#116 · Filter by author Marcosis2 opened on Apr 10, 2026

• Recommended parameters for asm-to-unitig graph alignment

  maickrau/GraphAligner#115 · Filter by author zxzhang8 opened on Dec 23, 2025

• Fatal protobuf error when providing seed file (.gam)

  maickrau/GraphAligner#114 · Filter by author IgnazioSpaccavento opened on Dec 2, 2025
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• what is bitvector mode ?

  maickrau/GraphAligner#113 · Filter by author shihjimmy opened on Nov 3, 2025

• how can i generate a seed gam format and give it into GraphAligner ?

  maickrau/GraphAligner#112 · Filter by author shihjimmy opened on Aug 12, 2025
  1

• Assertion failure about scoreEnd vs. scoreHere in GraphAligner 1.0.20

  maickrau/GraphAligner#111 · Filter by author adamnovak opened on Jul 8, 2025
  4

• Mapping assemblies to pangenome graph

  maickrau/GraphAligner#110 · Filter by author Buuxx opened on Jul 2, 2025

• How to add read quality scores back into GAM

  maickrau/GraphAligner#107 · Filter by author BaxW opened on Sep 29, 2024
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• GraphAligner slow on R10 reads mapped to hprc graph

  maickrau/GraphAligner#106 · Filter by author xchang1 opened on Sep 27, 2024
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• GraphAligner closes named pipe (feature request)

  maickrau/GraphAligner#105 · Filter by author nrizzo opened on Aug 27, 2024
  2

• Unable to reproduce alignment speed in the GraphAligner publication

  maickrau/GraphAligner#104 · Filter by author jzhang-dev opened on Aug 12, 2024

• multiple mapping

  maickrau/GraphAligner#96 · Filter by author yjk-bertrand opened on Jan 19, 2024
  2

• Incorrect alignments, assertion errors with --seedless-DP when read has a mismatch in the first base

  maickrau/GraphAligner#93 · Filter by author shenker opened on Oct 2, 2023

• Allow compilation with latest dependencies from conda-forge

  maickrau/GraphAligner#92 · Filter by author shenker opened on Oct 2, 2023
  1

• Several issues about installsion version,compile,and assertion.

  maickrau/GraphAligner#91 · Filter by author linsindian opened on Sep 19, 2023

• Alignments jumping haplotype?

  maickrau/GraphAligner#89 · Filter by author skoren opened on Aug 31, 2023

• Doesn't GraphAligner support .vg graph?

  maickrau/GraphAligner#87 · Filter by author tanger-code opened on Aug 14, 2023
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• unmapped reads

  maickrau/GraphAligner#86 · Filter by author asylvz opened on Jul 13, 2023
  1

• Alignment error

  maickrau/GraphAligner#83 · Filter by author GeorgeBGM opened on Jun 13, 2023
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• GAM surject incompatible with VG

  maickrau/GraphAligner#82 · Filter by author jiadong324 opened on May 15, 2023
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• Expected alternative alignment not shown

  maickrau/GraphAligner#78 · Filter by author JianjunJin opened on Mar 7, 2023
  4

• Memory and threads suggested - Core dump when building minimizer seeder from the graph

  maickrau/GraphAligner#72 · Filter by author lingliao opened on Dec 8, 2022
  8

• Can we add python to the docker image graphaligner

  maickrau/GraphAligner#71 · Filter by author lingliao opened on Dec 2, 2022

• GraphAligner fails with large number of threads

  maickrau/GraphAligner#68 · Filter by author TanyaDvorkina opened on Sep 30, 2022
  3