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RAILS v1.4 and cobbler v0.5
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@warrenlr warrenlr released this 13 Apr 15:23
· 42 commits to master since this release
v1.4
5b9c4bf

RAILS v1.4 and cobbler v0.5
Overall better read handling for gap-filling and scaffolding

  1. Save in memory gap sequence (patch), from highest-matching read for both tools
  2. Track #reads support in cobbler (-l) and RAILS, and allow cutoff when scaffolding (-l and -a), with latter (RAILS)
  3. Remove the hardcoded two-hit requirement for a read in RAILS. Instead, process two best hits for each read aligning different sequences
  4. Implement grace (-g) option, which effectively simulate read trimming (valuable for ONT mapping)
  5. bug fixes (-list.tsv (cobbler) reported some instances of gap-fill regions not fixed in the assembly – very marginal ~2.4% discrepancy). cobbler gap-fill table now lists the number of supporting reads for each gap filled
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