LSC

  • LSC is a long read error correction tool.
    It offers fast correction with high sensitivity
    and good accuracy.
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Latest News: Major update version 2.0 ... read more

FAQ

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What is LSC?

LSC is a program written entirely in python2.6 that is able to correct the thrid generation long reads by the second generation short reads.

[ LSC 0.2.4 ] What is in the folder "output_old"?

  • Question:
  • I got three folders output, output_old, and temp. I guess LSCoutput is new vision result and LSCoutput_old is earlier vision result. Right? New result folder has new files like newLS.fa etc. Could you explain the files mean?
  • Answer:
  • The folder output_old contains some "old" results which may have slightly lower accuracy. In LSC 0.2.4, I corrected some bugs and output "new" results in the folder output. You should use these files. newLS.fa is just a temp file for debugging. you only need to use full_LR_SR.map.fa and corrected_LR_SR.map.fa

"awk" bugs?

  • Question:
  • LSC 0.2.1 runs fine on a small set of data, but when it runs on the whole short read set (49 GB) I get an read error in awk:
    (awk: read error (Bad address)	
    At first try it reached 30 GB but this error popped up earlier and earlier with each run. This error also appears when I just run awk from the commandline on this set.
  • Answer:
  • The user may have used mawk that is a very fast AWK implementation by Mike Brennan based on a byte code interpreter. You will install GNU awk to run LSC.