sga
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jts
de novo sequence assembler using string graphs
The correction of ONE insertion leads to MANY base changes, because all bases following the insertion are shifted. Reported metrics represent base changes, not base corrections. Thank you for providing...
Strand bias of errors is an interesting aspect of read QC. It should not be too difficult to add something to preqc that measures/quantifies this (he said naively)...
http://www.software.ac.uk/software-evaluation-guide http://software.ac.uk/sites/default/files/SSI-SoftwareEvaluationCriteria.pdf If you're feeling gutsy :-)
Needs help text if nothing is passed in Needs to be able to suppress `-r' being passed to sga merge Have option to run the jobs in sequential (locally) instead...
While running sga index I get this: ``` Building index for preprocessed.fastq in memory using ropebwt done bwt construction, generating .sai file sga: SampledSuffixArray.cpp:163: void SampledSuffixArray::buildLexicoIndex(const BWT*, int): Assertion `numStrings...
This should be fixed by making the documentation/output clear or by using one of the new forward-index only overlap algorithms (like in KmerOverlaps.h).
With barcoding included in headers of recent Illumina output it would be nice to keep this information for each sequence in final output. Currently this is screened out in Utils/SeqReader.cpp...
Merging sequences prior to sga assemble losing the vertex coverage information. This information must be kept to avoid popping bubbles and retaining the lower-coverage branch.