katerinakazantseva/strainy

Issues

• Output GFA missing unitigs in S lines

  #73 opened a year ago by atabeerk
  13

• amplicon ONT sequencing of 740 known strains

  #85 opened 2 months ago by weishwu
  2

• FASTA to GFA

  #84 opened 3 months ago by juanjo255
  4

• Split `transform.py`

  #36 opened 3 months ago by mikolmogorov
  0

• Make installable as python package

  #35 opened 4 months ago by mikolmogorov
  0

• Issue with Running Strainy - ModuleNotFoundError: No module named 'flye.six.moves'

  #81 opened 5 months ago by GuillermoIllan
  3

• Low coverage - output files missing

  #80 opened 8 months ago by brambloemen
  4

• Cache the contents of the file, not the path

  #58 opened 8 months ago by atabeerk
  1

• make -C submodules/Flye error

  #71 opened 8 months ago by Penny2023James
  4

• Import flye as python package

  #48 opened 9 months ago by mikolmogorov
  1

• Skip / downsample unitigs with very high coverage

  #52 opened 9 months ago by mikolmogorov
  1

• Transform stage occasionally crashes with >16 threads

  #75 opened 10 months ago by Mikes92
  22

• gfapy.error.NotFoundError

  #70 opened 2 years ago by mallen6
  2

• Phased bam error

  #53 opened 2 years ago by jsgounot
  6

• Fix Pandas SettingWithCopyWarning

  #30 opened 2 years ago by mikolmogorov
  0

• Speed-up and parallel transform

  #40 opened 2 years ago by mikolmogorov
  0

• Automatically split very long graph unitigs

  #39 opened 2 years ago by mikolmogorov
  0

• Use `spawn` to create processes on Mac

  #34 opened 2 years ago by mikolmogorov
  1

• Might get some speed up using Pyston

  #50 opened 2 years ago by jelber2
  0

• samtools merge fails with `too many open files`

  #33 opened 2 years ago by mikolmogorov
  1

• Clean up code + terminal output

  #41 opened 2 years ago by mikolmogorov
  3

• Flye as submodule

  #29 opened 2 years ago by mikolmogorov
  1

• No need for extra fasta file input (-f argument)

  #37 opened 2 years ago by mikolmogorov
  0

• Improve manual

  #31 opened 2 years ago by mikolmogorov
  4

• gfapy merging fails occasionally

  #38 opened 2 years ago by mikolmogorov
  1

• Don't use wildcard imports + parameters naming

  #32 opened 2 years ago by mikolmogorov
  0

• Faster pairwise alignment

  #4 opened 2 years ago by mikolmogorov
  1

• Raise error if bam index is missing

  #3 opened 2 years ago by mikolmogorov
  1

• Output directory as a parameter.

  #2 opened 2 years ago by mikolmogorov
  1

• Command line agruments

  #1 opened 2 years ago by mikolmogorov
  1