bin/create_graphs.rb
bin/extract_seqs.rb
bin/extract_seqs_from_fasta.rb
bin/extract_seqs_from_fastq.rb
bin/fasta2fastq.rb
bin/fastq2fasta.rb
bin/gen_qual.rb
bin/get_seq.rb
bin/group_by_range.rb
bin/join_ilumina_paired.rb
bin/parse_amplicons.rb
bin/parse_json_results.rb
bin/parse_params.rb
bin/resume_clusters.rb
bin/resume_rejected.rb
bin/reverse_paired.rb
bin/seqtrimnext
bin/split_fastq.rb
bin/split_ilumina_paired.rb
bin/split_paired.rb
lib/seqtrimnext/actions/action_ab_adapter.rb
lib/seqtrimnext/actions/action_ab_far_adapter.rb
lib/seqtrimnext/actions/action_ab_left_adapter.rb
lib/seqtrimnext/actions/action_empty_insert.rb
lib/seqtrimnext/actions/action_ignore_repeated.rb
lib/seqtrimnext/actions/action_indetermination.rb
lib/seqtrimnext/actions/action_induced_low_complexity.rb
lib/seqtrimnext/actions/action_insert.rb
lib/seqtrimnext/actions/action_is_contaminated.rb
lib/seqtrimnext/actions/action_key.rb
lib/seqtrimnext/actions/action_left_adapter.rb
lib/seqtrimnext/actions/action_left_primer.rb
lib/seqtrimnext/actions/action_linker.rb
lib/seqtrimnext/actions/action_low_complexity.rb
lib/seqtrimnext/actions/action_low_high_size.rb
lib/seqtrimnext/actions/action_low_quality.rb
lib/seqtrimnext/actions/action_mid.rb
lib/seqtrimnext/actions/action_multiple_linker.rb
lib/seqtrimnext/actions/action_paired_reads.rb
lib/seqtrimnext/actions/action_poly_a.rb
lib/seqtrimnext/actions/action_poly_t.rb
lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
lib/seqtrimnext/actions/action_right_adapter.rb
lib/seqtrimnext/actions/action_right_primer.rb
lib/seqtrimnext/actions/action_short_insert.rb
lib/seqtrimnext/actions/action_unexpected_poly_t.rb
lib/seqtrimnext/actions/action_unexpected_vector.rb
lib/seqtrimnext/actions/action_vectors.rb
lib/seqtrimnext/actions/seqtrim_action.rb
lib/seqtrimnext/classes/action_manager.rb
lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb
lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb
lib/seqtrimnext/classes/extract_stats.rb
lib/seqtrimnext/classes/gnu_plot_graph.rb
lib/seqtrimnext/classes/graph_stats.rb
lib/seqtrimnext/classes/install_database.rb
lib/seqtrimnext/classes/install_requirements.rb
lib/seqtrimnext/classes/list_db.rb
lib/seqtrimnext/classes/make_blast_db.rb
lib/seqtrimnext/classes/one_blast.rb
lib/seqtrimnext/classes/params.rb
lib/seqtrimnext/classes/piro.rb
lib/seqtrimnext/classes/plugin_manager.rb
lib/seqtrimnext/classes/scan_for_restr_site.rb
lib/seqtrimnext/classes/scbi_stats.rb
lib/seqtrimnext/classes/seqtrim.rb
lib/seqtrimnext/classes/sequence.rb
lib/seqtrimnext/classes/sequence_group.rb
lib/seqtrimnext/classes/sequence_with_action.rb
lib/seqtrimnext/plugins/plugin.rb
lib/seqtrimnext/plugins/plugin_ab_adapters.rb
lib/seqtrimnext/plugins/plugin_adapters.rb
lib/seqtrimnext/plugins/plugin_amplicons.rb
lib/seqtrimnext/plugins/plugin_contaminants.rb
lib/seqtrimnext/plugins/plugin_extract_inserts.rb
lib/seqtrimnext/plugins/plugin_find_poly_at.rb
lib/seqtrimnext/plugins/plugin_ignore_repeated.rb
lib/seqtrimnext/plugins/plugin_indeterminations.rb
lib/seqtrimnext/plugins/plugin_key.rb
lib/seqtrimnext/plugins/plugin_linker.rb
lib/seqtrimnext/plugins/plugin_low_complexity.rb
lib/seqtrimnext/plugins/plugin_low_high_size.rb
lib/seqtrimnext/plugins/plugin_low_quality.rb
lib/seqtrimnext/plugins/plugin_mids.rb
lib/seqtrimnext/plugins/plugin_rem_adit_artifacts.rb
lib/seqtrimnext/plugins/plugin_short_insert.rb
lib/seqtrimnext/plugins/plugin_vectors.rb
lib/seqtrimnext/templates/amplicons.txt
lib/seqtrimnext/templates/genomics_454.txt
lib/seqtrimnext/templates/genomics_454_with_paired.txt
lib/seqtrimnext/templates/low_quality.txt
lib/seqtrimnext/templates/low_quality_and_low_complexity.txt
lib/seqtrimnext/templates/transcriptomics_454.txt
lib/seqtrimnext/templates/transcriptomics_plants.txt
lib/seqtrimnext/utils/extract_samples.rb
lib/seqtrimnext/utils/fasta2xml.rb
lib/seqtrimnext/utils/global_match.rb
lib/seqtrimnext/utils/hash_stats.rb
lib/seqtrimnext/utils/json_utils.rb
lib/seqtrimnext/utils/load_fasta_names_in_hash.rb
lib/seqtrimnext/utils/load_qual_in_hash.rb
lib/seqtrimnext/utils/recover_mid.rb
lib/seqtrimnext/utils/string_utils.rb
lib/seqtrimnext.rb
History.txt
Manifest.txt
PostInstall.txt
Rakefile
README.rdoc
script/console
script/destroy
script/generate
test/test_helper.rb
test/test_seqtrimnext.rb