Bioinformatics Tools

Browse all available bioinformatics tools.

Available tools

Alignment Gap Open Extension One Run Tool One affine gap run with an explicit choice whether extension is charged on its first position.
BAM CIGAR Opcode Length Split Tool Decode one unsigned BAM CIGAR word: low four bits select the operation and the upper bits encode positive length.
BAM Flag Strand Token Tool Read SAM flag bit 0x10 only; this does not infer biological transcript strand.
BED Twelve Block Relative Start Term Tool One BED12 block uses a zero-based offset relative to chromStart and a half-open absolute interval.
BED Zero To Start Convert one nonempty zero-based half-open BED interval to one-based inclusive coordinates; empty intervals are outside this conversion.
Bioinformatics: Codon Ambiguity Position Mask Tool Inspect one uppercase DNA IUPAC codon for ambiguous nucleotide positions counted from one; no translation, strand inference or sequence generation.
Bioinformatics: Fastq Quality Char Phred Score Tool Decode one printable FASTQ quality character under explicitly selected historical ASCII offset33 or64, without auto-detecting encoding or validating a read.
Bioinformatics: GFF Phase Token Check Tool Parse one GFF3 phase token 0/1/2 or unknown dot, retaining unknown status; does not infer CDS frame or validate an entire feature.
Bioinformatics: VCF Symbolic Alt Label Tool Classify a restricted VCF ALT as a symbolic angle identifier, spanning-deletion star or nucleotide literal; excludes breakend grammar and biological interpretation.
CDS Frame Offset Compute zero-based codon offset from an explicit spliced-CDS base count, distinct from a GFF phase field.
CIGAR Reference Consumption Gap Tool Count SAM reference-consuming operations and compare an explicit span; alignment placement constraints are outside this operation counter.
CIGAR Skipped Reference Length Tool Sum only CIGAR N reference-skip lengths; D deletions and other reference-consuming operations are excluded.
CIGAR Soft Clip Length Tool Sum S operation lengths in a supplied CIGAR operation stream; alignment-level clipping placement checks are separate.
Codon Degeneracy Supplied Code Record Tool Count matching codons in an explicit caller-supplied genetic-code record; no organism-specific code is assumed.
Codon Start Stop Source Tag Record an explicit codon role and genetic-code source without assigning start or stop status across code tables.
FASTA Accession Version Suffix Split a final dot plus numeric accession version from supplied FASTA identifier text without validating an accession registry.
FASTA Header Accession Split Split one FASTA definition line into the first whitespace-delimited identifier and remaining literal description without resolving an accession registry.
FASTA Iupac Ambiguity Cardinality Tool Uppercase IUPAC DNA ambiguity codes, excluding RNA U, gaps and unknown punctuation.
FASTA Non Sequence Label Gap Tool Classify supplied FASTA-like lines under an explicit header prefix and alphabetic sequence subset; no biological alphabet validation.
FASTQ Header Pair Index Token Preserve an explicitly supplied FASTQ read pair index and source format without inferring a header dialect.
FASTQ Quality Trimming One End Budget Tool Trim only the consecutive below-threshold quality run at one selected end; internal low scores are retained.
Genomic Insertion Interbase Coordinate Represent an insertion after the supplied one-based left base as a zero-based interbase boundary; zero denotes before the first base.
Genomic Left Closed Right Open Length Term Tool Zero-based half-open interval length with -1 as the no-last-position sentinel for an empty interval.
Genomic Strand Sign Crosswalk Map explicit +/−/unknown genomic strand notation to a signed value with a separate known flag.
GFF3 Phase Strand Carry Tool Carry CDS phase along transcript direction using supplied feature length; minus-strand phase is measured from the feature end.
GTF Escaped Quote Attribute Token Tool Quote one GTF-style attribute value by escaping backslash and double quote; reject control characters.
GTF Quoted Attribute Token Format a single GTF name and quoted attribute value, rejecting quote, backslash and line-control characters instead of inventing an escape dialect.
Kmer Canonical Reverse Complement Pair Tool Canonical uppercase DNA k-mer is the ASCII-lexicographically smaller of the k-mer and its reverse complement.
Phased Genotype Missing Count Tool Inspect VCF allele missingness and literal phase separators; no genotype likelihood or biological phasing inference.
Phasing Block Span Tool Count supplied genomic coordinate span under an explicit endpoint convention, without inferring phase.
Phred Error Odds Tool Convert a supplied Phred score to error probability and finite error odds, preserving the Q=0 undefined-odds flag.
Pileup Readstart Quality Symbol Tool Decode the mapping-quality character immediately following a pileup read-start caret using Phred+33.
Protein Residue Position Label Label an explicitly supplied protein residue symbol and one-based position without checking a sequence or inferring a substitution.
Protein Stop Symbol Terminal Policy Tool Check stop-symbol placement in an uppercase protein token; residue-alphabet validation beyond uppercase spelling is outside this policy.
Reverse Strand One Coordinate Transform Tool Reflect a zero-based base index within a sequence, rather than converting a one-based coordinate.
SAM CIGAR Zero Length Flag Tool Flag zero-length operations in a supplied parsed CIGAR stream; no alignment or sequence is reconstructed.
SAM Mate Unmapped Position Policy Tool SAM bit 0x8 reports an unmapped mate even when its coordinate fields carry a placement anchor; do not infer mapping from position alone.
SAM Optional Field Type Token Split a SAM optional field lexical TAG:TYPE:VALUE token without validating the type-specific value payload.
VCF Allele Index Reference Alternate Token Tool Map a normalized genotype allele index, using -1 for the missing allele sentinel; no biological variant interpretation.
VCF Break End Orientation Token Tool Parse the common ASCII-contig, ACGTN-sequence paired-breakend subset into literal bracket and sequence placement; no rearrangement inference.
VCF Genotype Allele Separator Flag Inspect explicit separators in a VCF 4.5 GT token, including an optional first phase indicator, preserving missing alleles without validating allele indices or inferring omitted indicators.
VCF Missing Genotype Ploidy Token Tool Count genotype allele slots including missing tokens; phased=true requires only pipe separators and at least two alleles.
VCF Reference Padding Count Tool Count literal common sequence-allele flanks without trimming, normalization or claims that every common base is mandatory VCF padding.