Transposable element assembler
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sparsehash
AUTHORS
INSTALL
LICENSE
README.md
assembler.cpp
assembler.hpp
doc.pdf
equations.cpp
equations.hpp
fastxParser.cpp
fastxParser.hpp
globals.cpp
globals.hpp
graphRepeatFinder.cpp
graphRepeatFinder.hpp
graphTrimmer.cpp
graphTrimmer.hpp
hashes.hpp
inclusionRemover.cpp
inclusionRemover.hpp
kmer.cpp
kmer.hpp
kmerCode.cpp
kmerCode.hpp
kmerIterator.cpp
kmerIterator.hpp
kmerSet.cpp
kmerSet.hpp
kmerVicinity.cpp
kmerVicinity.hpp
loopOpener.cpp
loopOpener.hpp
makefile
murmur.cpp
murmur.hpp
optionparser.h
rational.cpp
rational.hpp
reducedKmerCount.hpp
repeatHolder.cpp
repeatHolder.hpp
repeatMerger.cpp
repeatMerger.hpp
repeats.cpp
repeats.hpp
scaffolder.cpp
scaffolder.hpp
sequence.cpp
sequence.hpp
sequenceComparator.cpp
sequenceComparator.hpp
sequenceGraph.cpp
sequenceGraph.hpp
sequenceMerger.hpp
simpleKmerCount.cpp
simpleKmerCount.hpp
simplex.cpp
simplex.hpp
tedna.cpp

README.md

Tedna 1.3.0

This is the Tedna repository.

It has first been published in Bioinformatics in 2014.

It also has been used in Molecular Ecology in 2018.

To use Tedna, clone it and type make.

Type ./tedna -h to get some info on the options.

If you have paired-end reads with insert size 300, you can type:

./tedna -1 left.fastq -2 right.fastq -k 61 -i 300 -o output.fasta

If you have long reads (such as PacBio), you can type:

./tedna -1 reads.fastq -k 61 -m 1000 -t 25 -o output.fasta

Previous versions are available from the URGI Website.

Do no hesitate to contact me for any further question.