GenomeHelper - A command Line program and Java API of helper tools for genomics

Use java -jar GenomeHelper.jar <program-name> -h for help with each program:

The following programs are available.

Fasta-related programs:

Usage: FastaMotifFinder fastaFile searchMotif motifCountsFile proteinCountsFile minCount
Usage: FastaGetLongestSubstring outfile.
Usage: FastaGetGenomeLength infile
Usage: FastaTranslate infile outfile
Usage: FastaGetGCContent fastafile
Usage: FastaGetSingleFromMultiFasta infileoutfile seqId subsequence_start (optional) subsequence_end (optional)
Usage: FastaSelectRandomSequences fastaIn numberOfRandomSeqs randomSeqsoutfile
Usage: FastaToFastq fastaIn fastqOut

Fastq-related programs:

Usage: FastqCompress fastqIn fastqOut.gz
Usage: FastqInterlace leftReads rightReads interlacedFastqFile singlesFile
Usage: FastqDeinterlace interlacedFastqFile leftReads rightReads leftSinglesFile rightSinglesFile
Usage: FastqInterlaceKnownPairs leftReads rightReads interlacedFastqFile
Usage: FastqJoin leftReads rightReads fastqJoinedFile fastqSinglesFile
Usage: FastqSplit joinedFastqFile leftPairdReads rightPairedReads
Usage: FastqMotifFinder fastqFile searchMotif motifCountsFile proteinCountsFile minCount
Usage: FastqGetPairedEndSequencesWithMotifMatch interlacedFastqFile searchMotif matchingFastqFiles
Usage: FastqGetPairedEndSequencesFromFile listFile fastqFileInLeft fastqFileInRight fastqFileOutLeft fastqFileOutRight
Usage: FastqGetSingleEndSequencesFromFile listFile fastqFileIn fastqFileOut
Usage: FastqToFasta fastqIn fastaOut
Usage: FastqTranslate fastqIn fastaOut includeOriginalDNASequence ('true' or 'false')
Usage: FastqCountNucleotides fastqIn
Usage: FastqFindKmer fastqIn kmer

Quality-control programs:

Usage: QCPairedReads fastqInLeft fastqInRight fastqLeftOut fastqrRightOut readLength format('sanger' or 'illumina') writeBadReads ('true' or 'false')
Usage: QCSingleEndReads fastqIn fastqOut readLength format('sanger' or 'illumina') writeBadReads ('true' or 'false')
Usage: QCInterlacedReads fastqIn fastqOut readLength format('sanger' or 'illumina') writeBadReads ('true' or 'false')
Usage: QCInterlacedReadsToPairs fastqIn fastqLeftOut fastqrRightOut readLength format('sanger' or 'illumina') writeBadReads ('true' or 'false')
Usage: QCJoinedReads fastqIn fastqLeftOut fastqrRightOut readLength format('sanger' or 'illumina') writeBadReads ('true' or 'false')
Usage: QCVerifyReads fastqIn
Usage: QCVerifyPairedEndReads fastqLeft fastqRight
Usage: QCRemoveKmerPairedReads fastqInLeft fastqInRight fastqLeftOut fastqrRightOut kmerFile
Usage: QCRemoveKmerSingleReads fastqIn fastqOut kmerFile

SAM/BAM-related programs:

Usage: BAMGetMappedPairedReads bamfile fastqInLeft fastqInRight fastqOutLeft fastqOutRight
Usage: BAMGetUnmappedPairedReads bamfile fastqInLeft fastqInRight fastqOutLeft fastqOutRight
Usage: BAMGetBothUnmappedPairedReads bamFile fastqInLeft fastqInRight fastqOutLeft fastqOutRight
Usage: BAMGetBothMappedPairedRead bamFile fastqInLeft fastqInRight fastqOutLeft fastqOutRight
Usage: BAMGetSingleUnmappedPairedReads bamFile fastqInLeft fastqInRight fastqOutLeft fastqOutRight
Usage: BAMGetSingleMappedPairedReads bamFile fastqInLeft fastqInRight fastqOutLeft fastqOutRight

GFF-related programs:

Usage: GFFGetMeanFeatureLengthWithSplicing gffFile featureName refSeq
Usage: GFFGetMeanFeatureLength gffFile featureName
Usage: GFFGetMeanFeatureLengthOfGeneIDs gffFile featureName fileOfIds
Usage: GFFCreateNonCodingGenome gffFile refSeq nonCodingGenome
Usage: GFFCreateCodingGenome gffFile featureName refSeq codingGenome
Usage: GFFGetMeanIntronLength gffFile featureName refSeq
Usage: GFFGetMeanTargetIntronLength gffFile featureName targets
Usage: GFFCalculateCodingRegion gffFile refSeq attribute
Usage: GFFGetStats gffFile refSeq attribute