08-07-2013: Big changes in LSC 0.3
08-07-2013: Big changes in LSC 0.3
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)
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)