noodles
Bioinformatics I/O libraries
oarfish
A fast, accurate and versatile tool for long-read transcript quantification
xan
The CSV magician
merlin-rna
— a pure-Rust genomic RNA gene finder (tRNA, tmRNA, rRNA)
coverm
Read coverage calculator for metagenomics
orphos-core
Core library for Orphos, a tool for finding protein-coding genes in microbial genomes
bed2gtf
A fast and memory efficient BED to GTF/GFF converter
predictosaurus
Uncertainty aware haplotype based genomic variant effect prediction
orphos-cli
Command-line interface for Orphos, a tool for finding protein-coding genes in microbial genomes
noodles-csi
Coordinate-sorted index (CSI) format reader and writer
bevy_flowfield_tiles_plugin
FlowField (vector field) pathfinding as a plugin to the Bevy game engine
ferro-hgvs
HGVS variant normalizer - part of the ferro bioinformatics toolkit
prodigal-rs
Prokaryotic gene prediction — Prodigal rewritten in Rust
rustygal
Prokaryotic Dynamic Programming Genefinding Algorithm (Rust reimplementation of prodigal)
intspan
Command line tools for IntSpan related bioinformatics operations
gtf_splice_index
A fast, splice-aware index for GTF/GFF annotations enabling efficient transcript and gene lookup for RNA-seq read mapping and quantification
trnascan-rs
reimplementation of tRNAscan-SE 2.0 for transfer-RNA detection, using the byte-parity infernox (Infernal) covariance-model engine. Argv-faithful drop-in CLI.
genepred
port for the GenePred format in Rust
bioassert
CLI tool for asserting properties of files in bioinformatics pipelines
seqa_core
Object store support for vcf, bam, fasta, bigwig, bigbed, gff, bed, bedgraph, gtf
hgvs-weaver
High-performance HGVS variant mapping and validation engine
gecco
Gene Cluster prediction with Conditional Random Fields
oxbow
Read conventional genomic file formats as data frames and more via Apache Arrow
bramble-rs
Project spliced genomic alignments into transcriptomic coordinates
rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
multiseqex
Multi-sequence extractor from FASTA using FAI indexing, with parallelism and flexible region input formats
gtfsort
An optimized chr/pos/feature GTF/GFF sorter using a lexicographic-based index ordering algorithm written in Rust
genemancer
Rust CLI toolkit for niche optimized genomics file processing and target-based variant workflows
microBioRust
Microbiology friendly bioinformatics Rust functions
vareffect-cli
CLI for vareffect — annotate genomic variants without Ensembl VEP
xloci
get sequences from 2bit/fa using bed/gtf/gff
genomicframe-core
High-performance genomics I/O and interoperability layer
noodles-gff
Generic Feature Format (GFF) reader and writer
gxf2bed
fastest GTF/GFF-to-BED converter chilling around
locus-tui
A terminal genome browser for BAM files
microbiorust-py
Python bindings for microBioRust Microbiology friendly bioinformatics Rust functions
refman
A command-line manager for bespoke reference datasets used in bioinformatic analyses
exon
A platform for scientific data processing and analysis
rust-ise
Fast Rust-native ISEScan-equivalent insertion-sequence (IS) scanner for bacterial (meta)genomes: rustygal ORFs + MMseqs2 profile search + native affine-SW terminal inverted repeats
filterx
A command line tool to filter data by using python-like syntax
ugv
Ultra-fast genome viewer for interactive exploration of genomic data
igv-rs
Interactive terminal genome viewer for FASTA / VCF / BAM / GFF / BED / bigWig / BEDPE. Includes a bundled-igv.js browser companion.
gffx
An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
toxannotator
tox annotator for ToxDB
Stellerator
Extract candidate fusion-supporting reads for target genes from indexed BAM files
fragtk
Fragment file toolkit
rsomics-intervals
BED algebra + interval index + GFF/GTF interval extraction for the rsomics-* tool family. Layer A primitive.
stats_on_gff3_ncbi
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc
genomemask
mask specific regions of a genome in any format
nwn-lib-rs
Parsing library and command-line tools for Neverwinter Nights 1 and 2 data files
araseq
model genomics
covar
Calls physically-linked mutation clusters from wastewater amplicon sequencing data
rust-featurecounts
A fast feature counting tool for prokaryotic RNA-seq analysis, compatible with featureCounts
stats_on_gff3
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns, CpG ratio, etc. Examples: stats_on_gff3 Homo_sapiens…
cyanea-io
File format parsing for the Cyanea bioinformatics ecosystem
filterx_info
The builtin function documentation library for filterx
filterx_source
The source library for filterx
filterx_engine
The engine library for filterx
bed2gff
BED-to-GFF3 parallel translator
granges
command line tool for genomic range operations
serde-gff
https://github.com/Mingun/serde-gff
serde-pod
https://github.com/Mingun/serde-pod
frag_gene_scan_rs
gene prediction model for short and error-prone reads
exon-gff
reading and writing GFF files with Exon
use-genomic-range
Primitive genomic range and interval vocabulary for RustUse
mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
use-annotation
Primitive annotation vocabulary for RustUse
noel
A GTF/GFF per gene non-overlapping exon length calculator
use-feature
Primitive sequence and genomic feature vocabulary for RustUse
seq-here
A fast tool for bio-sequence file processing
roers
prepare augmented annotations for single-cell RNA-seq analysis
grangers
working with genomic ranges and annotations
tr-finder
genomers
Package to download NCBI genome data and metadata
gene-seq-intersections
Count intersections between genes and sequences
tuni
Unify transcripts across different samples
filterx_core
The core library for filterx
tca
A platform for scientific data processing and analysis
to-trans
A high-performance transcriptome builder from fasta + GTF/GFF
ncrs
A lightweight Rust library for loading and storing nucleic acid sequences (DNA or RNA) and their annotations with minimum dependences
exon-test
Exon test crate
nclist
finding overlapping intervals using a nested containment list
gffkit
program for gff3 file manipulation
gff_diff
generate a diff (in JSON format) between two GFF3 files
gxf2chrom
Everything in .chrom from GTF/GFF
gff
GFF game format packer/parser library
currycompose
providing a trait for performing currying (and non-currying) function-composition in rust
brrrr-lib
About Tools to process biological sequences and annotations to modern file formats
nwnrs
Command-line inspection, conversion, packing, unpacking, and NWScript tooling for Neverwinter Nights resources
nwnrs-types
Neverwinter Nights typed formats, resource systems, and tooling helpers
gff-derive
GFF game format packer/parser library: derive crate
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