.gitignore
.travis.yml
CITATION.md
Gemfile
LICENSE
README.md
Rakefile
bin/transrate
deps/blast.yaml
deps/deps.yaml
docs/transrate_logo_full.png
ext/transrate/extconf.rb
ext/transrate/transrate.c
files.txt
lib/transrate.rb
lib/transrate/assembly.rb
lib/transrate/cmd.rb
lib/transrate/cmdline.rb
lib/transrate/comparative_metrics.rb
lib/transrate/contig.rb
lib/transrate/contig_metrics.rb
lib/transrate/read_metrics.rb
lib/transrate/salmon.rb
lib/transrate/score_optimiser.rb
lib/transrate/snap.rb
lib/transrate/transrater.rb
lib/transrate/version.rb
lib/transrate/writer.rb
packaging/build_deps_linux.sh
packaging/build_deps_macosx.sh
packaging/bundler-config
packaging/minify.sh
packaging/transrate
test/data/150uncovered.l.fq
test/data/150uncovered.r.fq
test/data/Os.protein.2.fa
test/data/Os.protein.fa
test/data/assembly.2.fa
test/data/assembly.fasta
test/data/bridging_reads.l.fastq
test/data/bridging_reads.r.fastq
test/data/sorghum_100.fa
test/data/sorghum_transcript.fa
test/data/test.sf
test/data/test_contig_nc1.fa
test/data/test_contig_nc2.fa
test/data/test_contig_nc3.fa
test/data/test_contig_nc4.fa
test/data/test_contig_nc5.fa
test/data/test_contig_nc6.fa
test/data/test_contig_nc7.fa
test/data/test_reference_aa1.fa
test/data/test_reference_nc1.fa
test/data/tiny.sam
test/helper.rb
test/test_assembly.rb
test/test_cmd.rb
test/test_cmdline.rb
test/test_comp_metrics.rb
test/test_contig.rb
test/test_contig_metrics.rb
test/test_inline.rb
test/test_optimiser.rb
test/test_read_metrics.rb
test/test_salmon.rb
test/test_snap.rb
test/test_transrate.rb
test/test_transrater.rb
test/vagrant/centos_6.5_64/Vagrantfile
test/vagrant/debian_7.4_64/Vagrantfile
test/vagrant/debian_7.4_64/provision.sh
test/vagrant/fedora_20_64/Vagrantfile
test/vagrant/fedora_20_64/provision.sh
test/vagrant/linux-x86_64/Vagrantfile
test/vagrant/osx/Vagrantfile
test/vagrant/ubuntu_12.04_64/Vagrantfile
test/vagrant/ubuntu_12.04_64/provision.sh
transrate.gemspec