The genomics-proteomics toolkit

INSTALL

1.1 Automatic installation with Conda

conda install -c cobilab gto --yes

1.2 Manual installation

git clone https://github.com/bioinformatics-ua/gto.git
cd gto/src/
make

Note, an already compiled version of GTO is available for 64 bit Linux OS in the bin/ directory.

GTO Programs

The GTO provides pipe support for easy integration with the majority of the tools. These include programs to shuffle, transform, simulate, compress, vizualize, among others. The GTO includes the following tools, divided by genomic data format type. The documentation of those tools is available here.

1. FASTQ tools

• 1.1 gto_fastq_to_fasta
• 1.2 gto_fastq_to_mfasta
• 1.3 gto_fastq_exclude_n
• 1.4 gto_fastq_extract_quality_scores
• 1.5 gto_fastq_info
• 1.6 gto_fastq_maximum_read_size
• 1.7 gto_fastq_minimum_quality_score
• 1.8 gto_fastq_minimum_read_size
• 1.9 gto_fastq_rand_extra_chars
• 1.10 gto_fastq_from_seq
• 1.11 gto_fastq_mutate
• 1.12 gto_fastq_split
• 1.13 gto_fastq_pack
• 1.14 gto_fastq_unpack
• 1.15 gto_fastq_quality_score_info
• 1.16 gto_fastq_quality_score_max
• 1.17 gto_fastq_quality_score_min
• 1.18 gto_fastq_cut
• 1.19 gto_fastq_minimum_local_quality_score_forward
• 1.20 gto_fastq_minimum_local_quality_score_reverse
• 1.21 gto_xs
• 1.22 gto_fastq_clust_reads
• 1.23 gto_fastq_complement
• 1.24 gto_fastq_reverse
• 1.25 gto_fastq_variation_map
• 1.26 gto_fastq_variation_filter
• 1.27 gto_fastq_variation_visual
• 1.28 gto_fastq_metagenomics

2. FASTA tools

• 2.1 gto_fasta_to_seq
• 2.2 gto_fasta_from_seq
• 2.3 gto_fasta_extract
• 2.4 gto_fasta_extract_by_read
• 2.5 gto_fasta_info
• 2.6 gto_fasta_mutate
• 2.7 gto_fasta_rand_extra_chars
• 2.8 gto_fasta_extract_read_by_pattern
• 2.9 gto_fasta_find_n_pos
• 2.10 gto_fasta_split_reads
• 2.11 gto_fasta_rename_human_headers
• 2.12 gto_fasta_extract_pattern_coords
• 2.13 gto_fasta_complement
• 2.14 gto_fasta_reverse
• 2.15 gto_fasta_variation_map
• 2.16 gto_fasta_variation_filter
• 2.17 gto_fasta_variation_visual

3. Genomic sequence tools

• 3.1 gto_genomic_gen_random_dna
• 3.2 gto_genomic_rand_seq_extra_chars
• 3.3 gto_genomic_dna_mutate
• 3.4 gto_genomic_extract
• 3.5 gto_genomic_period
• 3.6 gto_genomic_count_bases
• 3.7 gto_genomic_compressor (also under the alias gto_geco)
• 3.8 gto_genomic_decompressor (also under the alias gto_gede)
• 3.9 gto_genomic_complement
• 3.10 gto_genomic_reverse (also under the alias gto_reverse)
• 3.11 gto_genomic_variation_map
• 3.12 gto_genomic_variation_filter
• 3.13 gto_genomic_variation_visual

4. Amino acid sequence tools

• 4.1 gto_amino_acid_to_group
• 4.2 gto_amino_acid_to_pseudo_dna
• 4.3 gto_amino_acid_compressor
• 4.4 gto_amino_acid_decompressor
• 4.5 gto_amino_acid_from_fastq
• 4.6 gto_amino_acid_from_fasta
• 4.7 gto_amino_acid_from_seq

5. General purpose tools

• 5.1 gto_char_to_line
• 5.2 gto_new_line_on_new_x
• 5.3 gto_upper_bound
• 5.4 gto_lower_bound
• 5.5 gto_brute_force_string
• 5.6 gto_real_to_binary_with_threshold
• 5.7 gto_sum
• 5.8 gto_filter
• 5.9 gto_word_search
• 5.10 gto_permute_by_blocks
• 5.11 gto_info
• 5.12 gto_segment
• 5.13 gto_comparative_map
• 5.14 gto_max
• 5.15 gto_min

6. External tools

The tools present in this section are from other authors that were considered top-performing tools with exelent features to aggregate in this toolkit. Please feel free to add more if you find it relevant.

• 6.1 gto_external_bfmem
• 6.2 gto_external_compareMEM
• 6.3 gto_external_copmem
• 6.4 gto_external_fastp
• 6.5 gto_external_formatconvert
• 6.6 gto_external_memoryfill
• 6.7 gto_external_minicom
• 6.8 gto_external_qvz
• 6.10 gto_external_spring

7. Scripts / Pipelines

The following shell scripts are examples of pipelines that combined some of this toolkit's features. More information available here

• 7.1 gto_build_dbs.sh
• 7.2 gto_complexity_profile_regions.sh
• 7.3 gto_complexity_profiles.sh
• 7.4 gto_create_viral_dataset.sh
• 7.5 gto_find_motif.sh
• 7.6 gto_map_rearrangements.sh
• 7.7 gto_map_rearrangements_proteins.sh
• 7.8 gto_metagenomics.sh
• 7.9 gto_proteins_complexity_profile_regions.sh
• 7.10 gto_simulate_rearragements.sh
• 7.11 gto_merge_fasta_dbs.sh
• 7.12 gto_build_xs_viral_db.sh
• 7.13 gto_create_sars_dataset.sh
• 7.14 gto_sars_simulation_detection.sh
• 7.15 gto_download_sars2.sh
• 7.16 gto_find_best_sars2.sh
• 7.17 gto_relative_complexity_profile.sh

CITE

Please cite the followings, if you use GTO:

GTO: A toolkit to unify pipelines in genomic and proteomic research. J. R. Almeida, A. J. Pinho, J. L. Oliveira, O. Fajarda, D. Pratas, SoftwareX, Volume 12, 2020, 100535, doi: https://doi.org/10.1016/j.softx.2020.100535

@article{ALMEIDA2020100535,
  title   = "GTO: A toolkit to unify pipelines in genomic and proteomic research",
  journal = "SoftwareX",
  volume  = "12",
  pages   = "100535",
  year    = "2020",
  issn    = "2352-7110",
  doi     = "https://doi.org/10.1016/j.softx.2020.100535",
  url     = "http://www.sciencedirect.com/science/article/pii/S2352711020301473",
  author  = "João R. Almeida and Armando J. Pinho and José L. Oliveira and Olga Fajarda and Diogo Pratas"
}

ISSUES

Please let us know if there is any issues.

LICENSE

GTO is under MIT license. For more information, click here.