Table 1.
Summary of 42 functions available in BioKIT at the time of publication.
| Function name | Description | Type of function | Input data | Citation | Example software that performs this function |
|---|---|---|---|---|---|
| alignment_length | Calculate alignment length | Analysis | Multiple-sequence file in FASTA format | NA | AMAS (Borowiec 2016) |
| alignment_recoding | Recode alignments using reduced character states | Processing | Multiple-sequence file in FASTA format | Woese et al. (1991), Embley et al. (2003), Kosiol et al. (2004), Hrdy et al. (2004), Susko and Roger (2007) | Custom scripts (Hernandez and Ryan 2021) |
| alignment_summary | Summarize diverse properties of a multiple sequence alignment | Analysis | Multiple-sequence file in FASTA format | NA | AMAS (Borowiec 2016); custom scripts (Shen, Salichos, et al. 2016); PhyKIT (Steenwyk, Buida, et al. 2021) |
| consensus_sequence | Generates a consensus sequence | Analysis | Multiple-sequence file in FASTA format | Sternke et al. (2019) | Geneious (https://www.geneious.com) |
| constant_sites | Determine the number of constant sites in an alignment | Analysis | Multiple-sequence file in FASTA format | Kumar et al. (2016) | IQ-TREE (Minh et al. 2020) |
| parsimony_ informative_sites | Determine the number of parsimony-informative sites in an alignment | Analysis | Multiple-sequence file in FASTA format | Kumar et al. (2016) | AMAS (Borowiec 2016); custom scripts (Shen, Salichos, et al. 2016) |
| position_specific_ score_matrix | Generates a position specific score matrix for an alignment | Analysis | Multiple-sequence file in FASTA format | Gribskov et al. (1987) | BLAST+ (Camacho et al. 2009) |
| variable_sites | Determine the number of variable sites in an alignment | Analysis | Multiple-sequence file in FASTA format | Shen, Salichos, et al. (2016) | AMAS (Borowiec 2016); custom scripts (Shen, Salichos, et al. 2016); PhyKIT (Steenwyk, Buida, et al. 2021) |
| gc_content_first_ position | Determine the GC content of the first codon position among protein coding sequences | Analysis | Protein coding sequences in FASTA format | Bentele et al. (2013) | Custom scripts (Bentele et al. 2013) |
| gc_content_second_ position | Determine the GC content of the second codon position among protein coding sequences | Analysis | Protein coding sequences in FASTA format | Bentele et al. (2013) | Custom scripts (Bentele et al. 2013) |
| gc_content_third_ position | Determine the GC content of the third codon position among protein coding sequences | Analysis | Protein coding sequences in FASTA format | Bentele et al. (2013) | Custom scripts (Bentele et al. 2013) |
| gene_wise_relative_ synonymous_ codon_usage | Calculate gene-wise relative synonymous codon usage | Analysis | Protein coding sequences in FASTA format | This study | This study |
| relative_synonymous_ codon_usage | Calculate relative synonymous codon usage | Analysis | Protein coding sequences in FASTA format | Xu et al. (2008) | MEGA (Kumar et al. 2016) |
| translate_sequence | Translate protein coding sequences to amino acid sequences | Processing | Protein coding sequences in FASTA format | NA | EMBOSS (Rice et al. 2000) |
| fastq_read_lengths | Examine the distribution of read lengths | Analysis | Sequence reads in FASTQ format | NA | FQStat (Chanumolu et al. 2019) |
| subset_pe_fastq_reads | Down sample paired-end reads | Processing | Sequence reads in FASTQ format | NA | SeqKit (Shen, Le, et al. 2016) |
| subset_se_fastq_reads | Down sample single-end reads | Processing | Sequence reads in FASTQ format | NA | SeqKit (Shen, Le, et al. 2016) |
| trim_pe_fastq_reads | Trim paired-end reads based on quality and length thresholds | Analysis | Sequence reads in FASTQ format | NA | Trimmomatic (Bolger et al. 2014) |
| trim_se_fastq_reads | Trim single-end reads based on quality and length thresholds | Analysis | Sequence reads in FASTQ format | NA | Trimmomatic (Bolger et al. 2014) |
| trim_pe_adapters_fastq_reads | Trim adapters from paired-end reads and implement length thresholds | Analysis | Sequence reads in FASTQ format | NA | Trimmomatic (Bolger et al. 2014) |
| trim_se_ adapters_fastq_reads | Trim adapters from single-end reads and implement length thresholds | Analysis | Sequence reads in FASTQ format | NA | Trimmomatic (Bolger et al. 2014) |
| gc_content | Determine GC content | Analysis | FASTA file of nucleotide sequences | Romiguier et al. (2010) | custom scripts (Shen, Salichos, et al. 2016); GC-Profile (Gao and Zhang 2006) |
| genome_assembly_metrics | Determine diverse properties of a genome assembly for quality assessment and characterization | Analysis | FASTA file of a genome assembly | Gurevich et al. (2013) | QUAST (Gurevich et al. 2013); REAPR (Hunt et al. 2013) |
| l50 | L50 | Analysis | FASTA file of a genome assembly | Gurevich et al. (2013) | QUAST (Gurevich et al. 2013) |
| l90 | L90 | Analysis | FASTA file of a genome assembly | Gurevich et al. (2013) | QUAST (Gurevich et al. 2013) |
| longest_scaffold | Determine the length of the longest entry in a FASTA file | Analysis | FASTA file | Gurevich et al. (2013) | Custom scripts (Ou et al. 2020) |
| n50 | N50 | Analysis | FASTA file of a genome assembly | Gurevich et al. (2013) | QUAST (Gurevich et al. 2013) |
| n90 | N90 | Analysis | FASTA file of a genome assembly | Gurevich et al. (2013) | QUAST (Gurevich et al. 2013) |
| number_of_large_scaffolds | Determine the number and length of scaffolds longer than 500 nucleotides. Length threshold of 500 nucleotides can be modified by the user | Analysis | FASTA file | NA | QUAST (Gurevich et al. 2013) |
| number_of_scaffolds | Determine the number of FASTA entries | Analysis | FASTA file | NA | QUAST (Gurevich et al. 2013) |
| sum_of_scaffold_lengths | Determine the total length of all FASTA entries | Analysis | FASTA file | NA | QUAST (Gurevich et al. 2013) |
| character_frequency | Determine the frequency of each character. Gaps are assumed to be represented as ‘?’ and ‘-’ characters | Analysis | FASTA file | NA | Biostrings (https://rdrr.io/bioc/Biostrings/) |
| faidx | Get sequence entry from FASTA file | Processing | FASTA file | NA | SAMtools (Li et al. 2009) |
| file_format_converter | Converts multiple sequence alignments from one format to another | Processing | FASTA, Clustal, MAF, Mauve, Phylip, Phylip-sequential, Phylip-relaxed, and Stockholm | NA | ALTER (Glez-Pena et al. 2010) |
| multiple_line_to_single_line_fasta | Reformat sequences to be represented on one line | Processing | FASTA file | NA | FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) |
| remove_fasta_entry | Remove sequence based on entry identifier | Processing | FASTA file | NA | NA |
| remove_short_sequences | Remove short sequences | Processing | FASTA file | NA | NA |
| rename_fasta_entries | Rename FASTA entries | Processing | FASTA file | NA | FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) |
| reorder_by_sequence_length | Reorder FASTA entries by length | Processing | FASTA file | NA | SeqKit (Shen, Le, et al. 2016) |
| sequence_complement | Generate sequence complements in the forward or reverse direction | Processing | FASTA file | Britten (1998) | EMBOSS (Rice et al. 2000) |
| sequence_length | Calculate the length of each FASTA file | Analysis | FASTA file | NA | bioawk (https://github.com/lh3/bioawk) |
| single_line_to_multiple_line_fasta | Reformat sequences to be represented on multiple lines | Processing | FASTA file | NA | FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) |