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The genomics-proteomics toolkit
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README.md

Build Status Codacy Badge License: MIT

GTO

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.

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. Scripts / Pipelines

6.1 gto_build_dbs.sh
6.2 gto_complexity_profile_regions.sh
6.3 gto_complexity_profiles.sh
6.4 gto_create_viral_dataset.sh
6.5 gto_find_motif.sh
6.6 gto_map_rearrangements.sh
6.7 gto_map_rearrangements_proteins.sh
6.8 gto_metagenomics.sh
6.9 gto_proteins_complexity_profile_regions.sh
6.10 gto_simulate_rearragements.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. bioRxiv 2020.01.07.882845; doi: https://doi.org/10.1101/2020.01.07.882845.

ISSUES

Please let us know if there is any issues.

LICENSE

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

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