08-07-2013: Big changes in LSC 0.3

[LSC]

08-07-2013: Big changes in LSC 0.3

http://www.stanford.edu/~kinfai/LSC/LSC.html

Many users met problems in downstream analyses by using the LSC output, because some output reads are only slightly-corrected, while others are well-corrected . In LSC 0.3, you have FASTQ output and also have correction score (SR length coverage percentage) to select the well-corrected reads for downstream analyses.

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

Very IMPORTANT updates:

Support for Bowtie2 and RazerS3 as initial aligners. Now, BWA, Bowtie2, RazerS3 and Novoalign work in LSC. Please see the comparison details of aligners in the "Short read - Long read aligner#manual".
Added SR length coverage percentage on LR (SR-covered length/full length of corrected LR) to corrected_LR output file. Here is an example, where the last number 0.82 is the SR length coverage percentage on LR:
>m111006_202713_42141_c100202382555500000315044810141104_s1_p0/18941/365_1361|0.82
Added support for three modes for step-wise runs:
mode 0: end-to-end
mode 1: generating LR_SR.map file
mode 2: correction step
Generating FASTQ output format based on correction probability given short read coverage. Please refer to LSC paper and manual page for more details. You can select well-corrected reads for downstream analyses by using the quality in FASTQ output or SR length coverage percentage above. Please the the filtering in the "Output#manual".

New features

Used the python path in the cfg file instead of default user/bin path
Added option (-clean_up) to remove intermediate files or not (Note: important/useful ones will still be there in temp folder)
Support for input fastq format for LR (long reads) and/or SR (short reads)
Updated default BWA and novoalign commands options
Printing out original LR names in the output file
Support for printing out version number using -v/-version option

Small bug fixed

Fixed in removing XZ pattern printed out at the end of some uncorrected_LR sequences
Fixed samParser bug (which was ignoring some valid alignments in BWA output)

[sparks]

Hi,

The options given for Novoalign are not ideal.

If you are using Novoalign with LSC you need to use -r Exhaustive not -r All. This will improve results dramatically and should be better than the other aligners.

For 100bp reads try

novoalign_options = -c1 -r Ex 1000 -t 120 -F FA -g 0 -x 20 -o sam

If read length is different adjust -t accordingly. On Cerebellum reads used by Kin Fai results are 40% better with 30% reduced run time vs BWA using LSC 0.3.1


Best, Colin