Sequential alignment function
SequentialAlignment(
lalista,
nodes,
readsPath,
GenomeFirstIndex,
GenomeSecondIndex,
outBam1,
outBam2,
threads,
outFormat,
phredScore,
maxExtractedSubreads,
consensusVote,
mismatchMax,
uniqueOnly,
maxMultiMapped,
indelLength,
fragmentMinLength,
fragmentMaxLength,
matesOrientation,
readOrderConserved,
coordinatesSorting,
allJunctions,
tempfolder,
readsAlignedBlock
)
list of samples
logic cores
sample folders
first genome index
second genome index
first output folder
second output folder
processes
BAM or SAM
quality score
number of subreads
consensus
mismatch
no multimapping
multimapping
indel
fragment minumum length
fragment maximum length
mate orientation
read order
sorting
junctions
temporary folder
chunks