Index

Symbols

--3-prime-quality ## oa-index command line option --5-prime-trim ## oa-index command line option --adapt3 adapt3 command line option oa-buildgraph command line option --adapt5 adapt5 command line option oa-buildgraph command line option --assmax BUILDGRAPH:ASSMAX command line option oa-buildgraph command line option --back ORGASM:BACK command line option oa-buildgraph command line option, [1], [2] --bad-quality ## oa-index command line option --bypass-filtering oa-index command line option --check-ids oa-index command line option --check-pairing oa-index command line option --check-phiX174 oa-index command line option --coverage BUILDGRAPH:COVERAGE command line option oa-buildgraph command line option, [1] --estimate-length #.## oa-index command line option --fasta oa-index command line option --fastq-dump oa-index command line option --forward-fasta oa-index command line option --kup ORGASM:KUP command line option oa-buildgraph command line option oa-seeds command line option --length ### oa-index command line option --low-memory oa-index command line option --lowcomplexity command line option oa-buildgraph command line option

--mate-pairs oa-index command line option --max-read ### oa-index command line option --mincov BUILDGRAPH:MINCOV command line option oa-buildgraph command line option --minimum-length ### oa-index command line option --minoverlap BUILDGRAPH:MINOVERLAP command line option oa-buildgraph command line option --minratio BUILDGRAPH:MINRATIO command line option oa-buildgraph command line option --minread BUILDGRAPH:MINREAD command line option oa-buildgraph command line option --no-check-phiX174 oa-index command line option --no-pipe oa-index command line option --quality-encoding-offset ## oa-index command line option --reformat oa-buildgraph command line option oa-index command line option --reverse-fasta oa-index command line option --seeds seeds oa-buildgraph command line option oa-seeds command line option --single oa-index command line option --skip ## oa-index command line option --smallbranches BUILDGRAPH:SMALLBRANCHES command line option oa-buildgraph command line option, [1] --snp command line option oa-buildgraph command line option -h, --help command line option oa-buildgraph command line option, [1], [2] oa-fasta command line option oa-index command line option oa-seeds command line option

A

Assembler (class in orgasm.assembler)

C

command line option --adapt3 adapt3 --adapt5 adapt5 --assmax BUILDGRAPH:ASSMAX --back ORGASM:BACK --coverage BUILDGRAPH:COVERAGE --kup ORGASM:KUP --lowcomplexity --mincov BUILDGRAPH:MINCOV --minoverlap BUILDGRAPH:MINOVERLAP --minratio BUILDGRAPH:MINRATIO --minread BUILDGRAPH:MINREAD --smallbranches BUILDGRAPH:SMALLBRANCHES --snp -h, --help forward index, [1] output reverse

coverageEstimate() (in module orgasm.tango) cutLowCoverage() (in module orgasm.tango) cutLowSeeds() (in module orgasm.tango)

F

fillGaps() (in module orgasm.tango) fillGaps2() (in module orgasm.tango)

forward command line option

G

getPairedRead() (in module orgasm.tango)

graph (orgasm.assembler.Assembler attribute)

I

index command line option, [1] oa-buildgraph command line option, [1], [2] oa-fasta command line option oa-seeds command line option

index (orgasm.assembler.Assembler attribute)

M

mode() (in module orgasm.tango)

O

oa-buildgraph command line option --adapt3 adapt3 --adapt5 adapt5 --assmax BUILDGRAPH:ASSMAX --back ORGASM:BACK, [1], [2] --coverage BUILDGRAPH:COVERAGE, [1] --kup ORGASM:KUP --lowcomplexity --mincov BUILDGRAPH:MINCOV --minoverlap BUILDGRAPH:MINOVERLAP --minratio BUILDGRAPH:MINRATIO --minread BUILDGRAPH:MINREAD --reformat --seeds seeds --smallbranches BUILDGRAPH:SMALLBRANCHES, [1] --snp -h, --help, [1], [2] index, [1], [2] output, [1], [2] oa-fasta command line option -h, --help index output oa-index command line option --3-prime-quality ## --5-prime-trim ## --bad-quality ## --bypass-filtering --check-ids --check-pairing --check-phiX174 --estimate-length #.## --fasta --fastq-dump --forward-fasta --length ### --low-memory --mate-pairs --max-read ### --minimum-length ### --no-check-phiX174 --no-pipe --quality-encoding-offset ## --reformat --reverse-fasta --single --skip ## -h, --help

oa-seeds command line option --kup ORGASM:KUP --seeds seeds -h, --help index output orgasm.assembler (module), [1] orgasm.tango (module), [1] output command line option oa-buildgraph command line option, [1], [2] oa-fasta command line option oa-seeds command line option

P

pairEndedConnected() (in module orgasm.tango)

path2fasta() (in module orgasm.tango)

R

readType() (orgasm.assembler.Assembler method)

reverse command line option

S

scaffold() (in module orgasm.tango)

seeds (orgasm.assembler.Assembler attribute)

U

unfoldAssembling() (in module orgasm.tango)