

set -ex



append_to_column_9_value.py -h
prepend_to_fasta_header.py -h
download_assemblies_from_genbank.py -h
convert_augustus_to_gff3.py -h
convert_gff3_to_ncbi_tbl.py -h
mark_partial_genes.py -h
filter_fasta_by_abundance.py -h
validate_feature_boundaries_on_molecules.py -h
add_polypeptide_to_gff3_gene_models.py -h
select_training_and_evaluation_transcripts.py -h
filter_fasta_by_type.py -h
filter_uniref_by_taxonomy.py -h
remove_orphaned_features.py -h
convert_blast_btab_to_bed.py -h
replace_gff_type_column_value.py -h
convert_blast_btab_to_gff3.py -h
interleave_fastq.py -h
split_isoforms_into_individual_genes.py -h
make_cufflinks_ids_unique.py -h
convert_gff3_to_gbk.py -h
make_go_slim_index.py -h
eggnog_to_sqlite3.py -h
convert_metagenemark_gff_to_gff3.py -h
append_to_fasta_header.py -h
merge_bam_files.py -h
remove_masked_gene_models.py -h
filter_fastq_by_N_content.py -h
uniref_to_sqlite3.py -h
uniprot_sprot_to_sqlite3.py -h
reverse_misordered_cds_coords.py -h
update_selected_column9_values.py -h
convert_gff3_to_gene_association_format.py -h
make_go_slim.py -h
join_columnar_files.py -h
split_interleaved_sequence_file.py -h
merge_masked_fasta_files.py -h
hmmlib_to_sqlite3.py -h
fasta_size_distribution_plot.py -h
report_gff3_statistics.py -h
reformat_fasta_residue_lengths.py -h
convert_cufflinks_gtf_to_gff3.py -h
list_biocode.py -h
fasta_simple_stats.py -h
fastq_simple_stats.py -h
convert_prodigal_to_gff3.py -h
convert_scipio_gff_to_gff3.py -h
filter_gff3_by_id_list.py -h
reorient_sequences_by_id.py -h
convert_fastq_to_fasta.py -h
create_rsem_html_table.py -h
convert_glimmerHMM_gff_to_gff3.py -h
convert_genbank_to_gff3.py -h
replace_homopolymeric_repeats_with_Ns.py -h
split_fasta_into_even_files.py -h
get_mpilup_from_id_list.py -h
convert_gff_to_ncbi_gff3.py -h
create_taxonomic_profile_from_blast.py -h
convert_fasta_contigs_to_gff3.py -h
merge_fasta_files_and_uniquify_ids.py -h
merge_predicted_gff3.py -h
filter_fasta_by_header_regex.py -h
convert_pasa_gff_to_models.py -h
extract_fasta_regions.py -h
set_source_column.py -h
tigrfam_info_to_sqlite3.py -h
add_gff3_locus_tags.py -h
fasta_base_content.py -h
subsample_fasta.py -h
convert_gff3_to_bed.py -h
compare_gene_structures.py -h
validate_fasta.py -h
randomly_subsample_fastq.py -h
append_to_fastq_read_header.py -h
convert_aat_btab_to_gff3.py -h
check_for_embedded_fasta_headers.py -h
convert_htab_to_bed.py -h
correct_gff3_CDS_phase_column.py -h
report_coverage_gaps.py -h
detect_inverted_repeats.py -h
convert_cegma_gff_to_gff3.py -h
remove_duplicate_features.py -h
remove_duplicate_sequences.py -h
create_taxonomy_db.py -h
calculate_query_coverage_by_blast.py -h
report_or_replace_nonstandard_residues.py -h
write_fasta_from_gff.py -h
filter_uniref_by_repid.py -h
check_gff_for_internal_stops.py -h
report_basic_gff_model_agreement.py -h
calculate_gene_coverage_from_assembly.py -h
report_gff_intron_and_intergenic_stats.py -h
extend_genes_to_stops.py -h
report_go_slim_counts.py -h
make_go_index.py -h
split_molecules_on_gaps.py -h
exit 0
