GTO is a toolkit for genomics and proteomics, namely for FASTQ, FASTA and SEQ formats, with many complementary tools. The toolkit is for Unix-based systems, built for ultra-fast computations. GTO supports pipes for easy integration with the sub-programs belonging to GTO as well as external tools. GTO works as LEGOs, since it allows the construction of multiple pipelines with many combinations.
GTO includes tools for information display, randomisation, edition, conversion, extraction, search, calculation, compression, simulation and visualisation. GTO is prepared to deal with very large datasets, typically in the scale of Gigabytes or Terabytes (but not limited). The complete toolkit is an optimised command-line version, using the prefix "gto_" followed by the suffix with the respective name of the program. GTO is implemented in C language and it is available, under the MIT license
Get GTO by installing them directly using the Cobilab channel from Conda:
conda install -c cobilab gto --yes
Or through the GitHub repository:
git clone https://github.com/cobilab/gto.git
cd gto/src/
make
Note, an already compiled version of GTO is available for 64 bit Linux OS in the bin/ directory.
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.
1.1 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_fastq_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
2.1 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 (also an alias to gto_fastq_variation_map)
2.16 gto_fasta_variation_filter (also an alias to gto_fastq_variation_filter)
2.17 gto_fasta_variation_visual (also an alias to gto_fastq_variation_visual)
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
3.8 gto_genomic_decompressor
3.9 gto_genomic_complement
3.10 gto_genomic_reverse
3.11 gto_genomic_variation_map (also an alias to gto_fastq_variation_map)
3.12 gto_genomic_variation_filter (also an alias to gto_fastq_variation_filter)
3.13 gto_genomic_variation_visual (also an alias to gto_fastq_variation_visual)
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
You can contribute to this project here .