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inDAGO (version 1.0.0)

SequentialAlignment: Sequential alignment function

Description

Sequential alignment function

Usage

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
)

Arguments

lalista

list of samples

nodes

logic cores

readsPath

sample folders

GenomeFirstIndex

first genome index

GenomeSecondIndex

second genome index

outBam1

first output folder

outBam2

second output folder

threads

processes

outFormat

BAM or SAM

phredScore

quality score

maxExtractedSubreads

number of subreads

consensusVote

consensus

mismatchMax

mismatch

uniqueOnly

no multimapping

maxMultiMapped

multimapping

indelLength

indel

fragmentMinLength

fragment minumum length

fragmentMaxLength

fragment maximum length

matesOrientation

mate orientation

readOrderConserved

read order

coordinatesSorting

sorting

allJunctions

junctions

tempfolder

temporary folder

readsAlignedBlock

chunks