A toolkit for DNA sequence analysis and manipulation.

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.

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.

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.

• Release 1.1

Please let us know if there is any issues.

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