algbio/practical-omnitigs

Issues

• Experiment fixes

  #210 opened 4 years ago by sebschmi
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• Remove scaffold gap misassemblies from unique misassemblies in QUAST

  #211 opened 4 years ago by sebschmi
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• Correctly assign the reads to the edges of wtdbg2

  #192 opened 4 years ago by sebschmi
  1

• Release 0.2.0

  #166 opened 4 years ago by sebschmi
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• Output safe walks as node sequences for wtdbg2

  #197 opened 4 years ago by sebschmi
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• Integrate the consensus stage from wtdbg2 into the pipeline

  #184 opened 4 years ago by sebschmi
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• Make existing assembly commands work with the wtdbg2 input formats

  #187 opened 4 years ago by sebschmi
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• Add option to heuristically compute the omnitigs of all SCCs

  #194 opened 4 years ago by sebschmi
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• Output omnitigs as .ctg.lay file for wtdbg2

  #186 opened 4 years ago by sebschmi
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• Load the wtdbg2 de Bruijn graph from the .1.nodes and .1.reads files as well as the reads

  #185 opened 4 years ago by sebschmi
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• Integrate the FDB graph generation from wtdbg2 into the pipeline

  #183 opened 4 years ago by sebschmi
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• Install and compile wtdbg2

  #182 opened 4 years ago by sebschmi
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• Read HamCycle instance files

  #168 opened 4 years ago by sebschmi
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• Evaluate HamCircuit preprocessing on random graphs

  #179 opened 4 years ago by sebschmi
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• Integrate different HamCycle solvers in the pipeline

  #171 opened 4 years ago by sebschmi
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• Contract node-centric omnitigs if possible, or output NO for HamCycle

  #170 opened 4 years ago by sebschmi
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• Add command to compute and preprocess random HamCycle instances and output them as some file format

  #176 opened 4 years ago by sebschmi
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• Generate random hamcycle instances

  #173 opened 4 years ago by sebschmi
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• Compute node-centric omnitigs

  #169 opened 4 years ago by sebschmi
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• There are more unitigs than edges/2

  #165 opened 4 years ago by sebschmi
  1

• Output statistics about omnitig length, omnitigs per macrotig

  #156 opened 4 years ago by sebschmi
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• Output statistics about macronodes per omnitig and macronodes per macrotig

  #163 opened 4 years ago by sebschmi
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• Create separate crate for sequence abstractions

  #161 opened 4 years ago by sebschmi
  1

• Make snakemake pipeline parallelisable

  #159 opened 4 years ago by sebschmi
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• Omnitigs are not filtered by reverse complement

  #154 opened 4 years ago by sebschmi
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• Add runtime statistics to algorithms

  #158 opened 4 years ago by sebschmi
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• Add the trivial omnitigs and omnitigs to our evaluation pipeline

  #153 opened 4 years ago by sebschmi
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• Additionally to omnitigs, output trivial omnitigs only (= Y-to-V transformation unitigs)

  #132 opened 4 years ago by sebschmi
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• Add command to compute maximal omnitigs

  #148 opened 4 years ago by sebschmi
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• Combine the whole pipeline that computes omnitigs into a single function call

  #147 opened 4 years ago by sebschmi
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• Extract trivial omnitigs that are not subwalks of non-trivial omnitigs

  #144 opened 4 years ago by sebschmi
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• Extract non-trivial omnitigs from macrotigs

  #143 opened 4 years ago by sebschmi
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• Track vapor in incremental hydrostructure to efficiently answer bridge-like query

  #137 opened 4 years ago by sebschmi
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• Add genome name to LaTeX file

  #138 opened 4 years ago by sebschmi
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• Make the verify-genome command output LaTeX optionally

  #101 opened 4 years ago by sebschmi
  1

• Output macrotig statistics in verify command

  #134 opened 4 years ago by sebschmi
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• Make snakemake assume bcalm2 output as ancient

  #139 opened 4 years ago by sebschmi
  1

• Compute hydrostructure incrementally

  #135 opened 4 years ago by sebschmi
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• Stitch together maximal microtigs to maximal macrotigs

  #123 opened 4 years ago by sebschmi
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• Compute maximal microtigs

  #122 opened 4 years ago by sebschmi
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• Refactor subgraph trait such that it can implement all the graph traits of its parent

  #129 opened 4 years ago by sebschmi
  1

• Filter records from input genomes

  #107 opened 4 years ago by sebschmi
  1

• Integrate Bandage into the pipeline

  #121 opened 4 years ago by sebschmi
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• Make the verify command output LaTeX optionally

  #99 opened 4 years ago by sebschmi
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• Convert the output of ContigValidator to LaTeX

  #97 opened 4 years ago by sebschmi
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• Document frequent conda error in installation

  #103 opened 4 years ago by sebschmi
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• Delete make_bcalm_output_deterministic.sh

  #104 opened 4 years ago by sebschmi
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• Convert the output of QUAST to LaTeX

  #98 opened 4 years ago by sebschmi
  1

• Remove pulp from environment.yml

  #112 opened 4 years ago by sebschmi
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• Clean up CLI command code

  #102 opened 4 years ago by sebschmi
  0