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: LSC 1.alpha -- faster and much less memory-required ... read more

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Copyright and installation instructions are contained within the package. We strongly recommend that you consult the tutorial before attempting to use LSC.

From LSC 0.3, we do not recommend you to use Novoalign any more, which makes LSC slow and lower sensitivity. However, you can still use it if you want to. Novoalign is developed by Novocraft and details can be found on it website.

LSC 1.alpha Please see the release notes for more information
LSC 0.3.1 Please see the release notes for more information
LSC 0.3 Please see the release notes for more information
LSC 0.2.4 Please see the release notes for more information
LSC 0.2.3 Please see the release notes for more information
LSC 0.2.2 Please see the release notes for more information
LSC 0.2.1 Please see the release notes for more information
LSC 0.2 Please see the release notes for more information

LSC 1.alpha - Release Notes

In the LSC 0.3.0 or 0.3.1, we optimized the setting of bowtie2 and BWA to get much more short read alignment, which improve the the accuracy of error correction a lot/ However, the increase of alignments also requires much more running time (on both alignment and the following error correction step) and memory usage. Therefore, a few users met difficulty of running LSC 0.3.0 or 0.3.1.

In LSC 1.alpha, we apply probabilistic algorithm ("SCD" option) to select ""enough" short read alignment for error correction. LSC 1.alpha does NOT sacrifice the error correction performace (sensitivity and specificity). Please see http://www.healthcare.uiowa.edu/labs/au/LSC/LSC_manual.html#aligner Thus, we save running time and memory usage significantly. The running time is 30-50% of LSC 0.3.1. The peak memory usage decreases to ~10G regardless of the data size.

New features:

Miscellaneous changes:

If you want to see the manual and tutorial of the old LSC (before 1.alpha), we keep the links of its the Old manual and Old tutorial in the right side bar.

LSC 0.3.1 - Release Notes

In LSC 0.3.1, we don't have pseudo chromosome, the alignment time reduced to ~10% (in Bowtie2 mode). And you can re-run some crashed jobs easily now.

New features:

Miscellaneous changes:

LSC 0.3 - Release Notes

In LSC 0.3, we have a few updates. They are very IMPORTANT updates, new features and small fixes

Very IMPORTANT updates:

New features

Small fixes

LSC 0.2.4 - Release Notes

1. Besides the default aligner Novoalign, BWA can be also used as the initial aligner from this version. Please find the new aligner options in the webpage ".cfg file format"

2. Some uncertain corrections may exsit at the right ends of the long reads in the old LSC. LSC 0.2.4 settles this problem and likely improves the accuracy further.

LSC 0.2.3 - Release Notes

If you run LSC at the bin folder (the bin folder is the work directory) or set the bin as the default path, then you may meet a bug. LSC 0.2.3 fixes this bug of finding the correct bin folder.

LSC 0.2.2 - Release Notes

LSC 0.2.2 fixes the bug of the option "I_RemoveBothTails". LSC 0.2.1 ran this option even if you set "N". It may halt the process in LSC 0.2.1 because the read name does not allow "RemoveBothTails". Now you can choose to use this option or not.

LSC 0.2.1 - Release Notes

LSC 0.2.1 fixes the bug of python path. Another bug of removing redundant reads is also fixed. LSC takes a long read data sets (>=100bp) and a short reads data sets (50 - 100bp) as input. They should be in FASTA format. Running time is almost linear with the the number of threads.

LSC 0.2 - Release Notes

LSC 0.2 takes a long read data sets (>=100bp) and a short reads data sets (50 - 100bp) as input. They should be in FASTA format. Running time is almost linear with the the number of threads.