A toolkit for DNA sequence analysis and manipulation.

INSTALL

Get GOOSE and make the project, using:

git clone https://github.com/pratas/goose.git
cd goose/src/
make

Note, an already compiled version of GOOSE is available for 64 bit Linux OS in the bin/ directory.

PROGRAMS

The GOOSE toolkit include the following programs:

goose-AminoAcidToGroup
goose-char2line
goose-comparativemap
goose-count
goose-extract
goose-extractreadbypattern
goose-fasta2seq
goose-fastaextract
goose-fastainfo
goose-fastq2fasta
goose-fastq2mfasta
goose-fastqclustreads
goose-FastqCut
goose-FastqExcludeN
goose-FastqInfo
goose-FastqMaximumReadSize
goose-FastqMinimumLocalQualityScoreForward
goose-FastqMinimumLocalQualityScoreReverse
goose-FastqMinimumQualityScore
goose-FastqMinimumReadSize
goose-FastqSplit
goose-FastqTrimm
goose-fastqpack
goose-fastqsimulation
goose-fastqtrimm
goose-fastqunpack
goose-filter
goose-findnpos
goose-geco
goose-gede
goose-genrandomdna
goose-getunique
goose-info
goose-max
goose-mfmotifcoords
goose-min
goose-minus
goose-mutatedna
goose-mutatefasta
goose-mutatefastq
goose-newlineonnewx
goose-period
goose-permuteseqbyblocks
goose-QSInfo
goose-QSMin
goose-QSMax
goose-randfastaextrachars
goose-randfastqextrachars
goose-randseqextrachars
goose-real2binthreshold
goose-reducematrixbythreshold
goose-renamehumanheaders
goose-reverse
goose-reverselm
goose-searchphash
goose-segment
goose-seq2fasta
goose-seq2fastq
goose-SequenceToGroupSequence
goose-splitreads
goose-sum
goose-UpperBound
goose-wsearch

GOOSE provides pipes support for easy integration with other pipelines. Moreover, there are many scripts to download sequences, shuffle, transform, etc.

CITE

Please cite the followings, if you use GOOSE:

• Manuscript of version 19 in preparation;
• J. R. Almeida, D. Pratas, A. J. Pinho. GOOSE: a toolkit for DNA sequence analysis and manipulation, 2018.

RELEASES

• Release 1.1

ISSUES

Please let us know if there is any issues.

LICENSE

GOOSE is under GPL v3 license. For more information, click here.