-
needletail
FASTX parsing and k-mer methods
-
rust-htslib
HTSlib bindings and a high level Rust API for reading and writing BAM files
-
gsearch
genome classification, probminhash hnsw, genome search
-
rasusa
Randomly subsample reads or alignments
-
plascad
PlasCAD
-
proseg
Probabilistic cell segmentation for in situ spatial transcriptomics
-
varfish-server-worker
Rust-based worker for varfish-server
-
noodles
Bioinformatics I/O libraries
-
grepq
quickly filter fastq files by matching sequences to a set of regex patterns
-
minimap2
Bindings to libminimap2
-
sgcount
A fast and flexible sgRNA counter
-
bed-reader
Read and write the PLINK BED format, simply and efficiently
-
lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
-
alignoth
creating alignment plots from bam files
-
block-aligner
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm
-
bio-seq
Bit packed and well-typed biological sequences
-
rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
-
rustyms
handle proteomic mass spectrometry data and match peptides to spectra
-
haddock-restraints
Generate restraints to be used in HADDOCK
-
intspan
Command line tools for IntSpan related bioinformatics operations
-
fasten
A set of scripts to run basic analysis on fastq files
-
fxtools
A collection of commandline Fasta/Fastq utility tools
-
finch
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
sourmash
tools for comparing biological sequences with k-mer sketches
-
rust-lapper
A fast and easy interval overlap library
-
atglib
handle transcripts for genomics and transcriptomics
-
simpleaf
framework to make using alevin-fry even simpler
-
light_phylogeny
Methods and functions for phylogeny
-
rustynetics
A high-performance genomics libary specialized in handling BAM and BigWig files
-
wdl
Lexing, parsing, validation, and linting for Workflow Description Language (WDL) documents
-
fqkit
cross-platform program for fastq file manipulation
-
nail
alignment inference tool
-
oarfish
A fast, accurate and versatile tool for long-read transcript quantification
-
hgvs
Port of biocommons/hgvs to Rust
-
sigalign
A Similarity-Guided Alignment Algorithm
-
sprocket
A package manager for the Workflow Description Language files
-
spiking_neural_networks
A package for designing and simulating biological neural network dynamics with neurotransmission
-
fqtk
A toolkit for working with FASTQ files
-
kmerutils
Kmer counting, hashing, sequence sketching
-
rdkit
High level RDKit functionality for rust
-
coprosize
coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models
-
slow5
interacting with slow5
-
crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
-
minimap2-temp
Bindings to libminimap2 (temporary fork)
-
kun_peng
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
-
rnapkin
CLI utility for drawing RNA secondary structure
-
verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
-
tsalign
A sequence-to-sequence aligner that accounts for template switches
-
compact-genome
Representation of genomes
-
give_a_sheet
Toolkit for generating input samplesheets for a variety of nf-core pipelines
-
genotype_cli
Genotype language CLI
-
galah
Microbial genome dereplicator
-
librna-sys
Low-level bindings for the ViennaRNA library
-
exon
A platform for scientific data processing and analysis
-
bustools
Interacting with the kallisto/bus format of scRNAseq data
-
scidataflow
A command-line tool to manage scientific research project data
-
fasta-stats
descriptive statistics on FASTA (biological sequence) data
-
consalifold
Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction
-
classeq-cli
A command line interface for the classeq library
-
coverm
Read coverage calculator for metagenomics
-
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…
-
atg
Convert transcripts between different file formats
-
varlociraptor
calling of genomic variants using a latent variable model
-
mehari
Variant effect prediction all in Rust
-
smyl
Artificial Neuronal Network in Rust
-
scattr
estimating the copy number of large tandem repeats
-
ggca
Computes efficiently the correlation (Pearson, Spearman or Kendall) and the p-value (two-sided) between all the pairs from two datasets
-
perbase
Fast and correct perbase BAM/CRAM analysis
-
mmft
A minimal fasta toolkit
-
parasail-rs
Rust bindings and wrapper for parasail, a SIMD C library for pairwise sequence alignment
-
ska
Split k-mer analysis
-
nohuman
Remove human reads from a sequencing run
-
rust-ena
ena-crate interacts directly with the European Nucleotide Archive(ENA)
-
wdl-format
Formatting of WDL (Workflow Description Language) documents
-
sufr
Parallel Construction of Suffix Arrays in Rust
-
abpoa-rs
Rust bindings for abPOA: Adaptive Banded POA
-
fastlin
an ultra-fast program for MTBC lineage typing
-
fastobo
Faultless AST for Open Biomedical Ontologies
-
chromsize
just get your chrom sizes
-
diced
reimplementation of the MinCED algorithm for identifying CRISPRs in full or assembled genomes
-
fire-fasta
Ultra-fast, lazy, zero-copy Multi-FASTA parser
-
fxread
A barebones fastx reader for rust
-
rust-sasa
RustSASA is a Rust library for computing the absolute solvent accessible surface area (ASA/SASA) of each atom in a given protein structure using the Shrake-Rupley algorithm
-
grumpy
Genetic analysis in Rust
-
fasta-filter
Filter a FASTA file and output a subset of the records on STDOUT
-
fakit
program for fasta file manipulation
-
flowtigs
An algorithm for calculating flowtigs in a De Bruijn graph of DNA reads in metagenomes
-
syntesuite
TODO
-
nwr
nwris a command line tool for newick and taxonomy -
gfatk
command line tool for manipulating small to medium sized GFA files, and specifically for output from the genome assembler MBG
-
psylink
GUI for PsyLink neural interface for receiving/graphing biosignals and predicting user's intentions
-
barkit-extract
extracting barcode nucleotide sequence according to a specified regex pattern
-
tsgen
A random genome generator that generates template switches
-
archaea
genome classification, probminhash hnsw archaea
-
bird_tool_utils
Microbial genomics utility functions
-
bed-utils
manipulating genomic range objects
-
seqdupes
Compress sequence duplicates
-
taxonomy
Routines for loading, saving, and manipulating taxonomic trees
-
omics-coordinate
Foundational representations of coordinates in the Rust omics ecosystem
-
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
-
genominicus
plot gene trees
-
seqsizzle
A pager for viewing FASTQ files with fuzzy matching, allowing different adaptors to be colored differently
-
biotest
Generate random test data for bioinformatics
-
seqkmer
sequence kmer
-
microBioRust
Microbiology friendly bioinformatics Rust functions
-
haptk
Haplotype analysis toolkit
-
genomap
A small library for storing generic genomic data indexed by a chromosome
-
dihardts_omicstools
Collection of different omic tools, structs and enums
-
yacrd
Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras
-
align-cli
A command line interface for easily aligning sequences
-
ggetrs
Efficient querying of biological databases from the command line
-
fastq
A parser for fastq
-
kseq
fasta/fastq format parser library
-
ecdna-lib
The ecDNA distribution for the evolutionary of extra-chromosomal DNA (ecDNA)
-
nucleob
bioinformatics: nucleobases and amino acids statistics
-
sumi
analysis for small RNA libraries with UMIs
-
ontime
Extract subsets of ONT (Nanopore) reads based on time
-
jam-rs
Just another (genomic) minhash (Jam) implementation in Rust
-
exon-fasta
reading and writing FASTA files with Exon
-
genotype_parser
Genotype language parser crate
-
fmlrc
FM-index Long Read Corrector - Rust implementation
-
lightdock
Macromolecular docking software based on the GSO algorithm
-
thermorawfilereader
A (relatively) high level interface to Thermo Fisher's RawFileReader library
-
noodles-gff
Generic Feature Format (GFF) reader and writer
-
bio-streams
Streaming bioinformatics data types
-
alevin-fry
A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data
-
wdl-analysis
Analysis of Workflow Description Language (WDL) documents
-
righor
creates model of Ig/TCR sequences from sequencing data
-
viguno
Phenotype/disease for VarFish
-
hmmsearch_rs
gene prediction, Hidden Markov models
-
rna-ss-params
RNA secondary structure parameters
-
lorikeet-genome
Strain resolver and variant caller via local reassembly for metagenomics
-
hyper-gen
HyperGen is a high-performance Rust library to sketch genomics files into hypervectors and realize fast Average Nucleotide Identity (ANI) approximation
-
classeq-watcher
watcher for the Classeq project
-
na_seq
DNA and RNA sequence types and functions
-
bustools_cli
Rust reimplementation of bustools for scRNAseq processing
-
rosella
Metagenome assembled genome recovery from metagenomes using UMAP and HDBSCAN
-
phylotree
deal with phylogenetic trees and distance matrices
-
tes
working with the Task Execution Service (TES) specification
-
msbwt2
multi-string BWT query library
-
hts-sys
HTSlib bindings
-
mni2mz3
Brain imaging surface mesh file format converter
-
motif_finder
Find motifs using Gibbs Sampler, Median String, and Randomized Motif Search algorithms in a fasta formatted file of reads Refer to the README to understand the input data
-
ncbitaxonomy
Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB
-
libdrugplotter
Easily compute drug concentration curves
-
lib3dmol
written in rust to read, manipulate, select atoms in protein structure files
-
fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
-
skani
fast tool for calculating ANI between metagenomic sequences, such as metagenome-assembled genomes (MAGs). It is extremely fast and is robust against incompleteness and fragmentation, giving accurate ANI estimates.
-
libwfa2
Bindings to the C implementation of WFA2-lib
-
smafa
Read aligner for small pre-aligned sequences
-
omics-molecule
Foundational representations of biological molecules in the Rust omics ecosystem
-
pdb-handler
functions to handle PDB files
-
orthanq
quantify haplotypes in an uncertainty-aware manner
-
bedrs
Genomic interval library in rust
-
psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
-
seal
Needleman-Wunsch & Smith-Waterman sequence alignment
-
codenano-server
editing DNA molecular designs in a browser
-
ambigviz
Identify and plot ambiguous nucleotide bases at given positions from a BAM file
-
fpa_lr
fpa filter long read mapping information to save disk space
-
oxbow
Read specialized bioinformatic file formats as data frames in R, Python, and more
-
sequence_domain
A DNA/RNA sequence domain
-
nthash
rolling hash function for hashing all possible k-mers in a DNA sequence
-
consalign
RNA Structural Aligner Based on Transfer-learning and Thermodynamic Ensemble Model
-
chainsaw
manipulate newick trees
-
gfautil
Command line tools for working with GFA files and related formats
-
hmmer-rs-2
Ergonomic Rust interface to HMMER
-
prole
collection of re-usable methods in Rust. Feel free to use them for your own work.
-
ncbi_dl
download ncbi genome file
-
genotype_lang_ts_tree
Genotype language TypeScript target AST crate
-
fasta_split
Split a fasta file into several fasta files
-
mpileup
Pile up multiple bam files site by site
-
bamrescue
check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
-
diced-py
PyO3 bindings and Python interface to the diced crate
-
ehxacto
Find exact tandem repeat coordinates from approximate regions identified by ExpansionHunter denovo
-
gdrs
GenomicDistributions package from bioconductor
-
fastleng
read length statistics tool
-
nwbview
Neurodata Without Borders viewer
-
elias_fano_rust
An optimized implementation of Sebastiano Vigna's Elis-Fano quasi succint datastructure
-
ffforf
fasta/q/x file format parser. Well fuzzed.
-
noodles-util
noodles support utilities
-
gffkit
program for gff3 file manipulation
-
finch_cli
min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
-
distance_aa
A backend for the distAAnce web application
-
heme
PDB reader and other protein modeling tools
-
seqrepo
Port of (read-only) functionality of biocommons/seqrepo to Rust
-
bio-jtools
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data
-
genome-graph
Representation of genome graphs
-
mutexpect
functions for determining potential point mutations in a genetic sequence and their statisical probability
-
diploid-contam-estimator
Estimating contamination level in diploid DNA seuqencing libraries
-
podders
Write uncompressed Pod5 files in native rust. No FFI! PODDDDERS
-
frag_gene_scan_rs
gene prediction model for short and error-prone reads
-
biofile
reading bioinformatics related files
-
lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
-
uniprot
Rust data structures and parser for the Uniprot database(s)
-
exon-benchmarks
Executable benchmarks for exon
-
drug-extraction-core
A core library for extracting drugs from text records
-
xdrfile
Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format.
-
cytos
A collection of frequently used Bioinformatics scripts/tasks written in Rust
-
noodles-cram
CRAM format reader and writer
-
efetch2jsonl
Convert EFetch XML to JSON Lines
-
prot_translate
Translate nucleotide sequence to protein
-
ppgg
associated executable, the library provides tools for building tools that can parse and work for VCF and FASTA files while the associated executable is a command line tool for generating…
-
slow5lib-sys
Low-level bindings to the slow5lib C library
-
entrez-rs
Rust wrapper for the Entrez API
-
barkit
— a cross-platform and ultrafast toolkit for barcodes manipulation in FASTQ files
-
gfa
working with graphs in the GFA (Graphical Fragment Assembly) format
-
nucleobases
low-level brick crate for managing nucleobases as data in code
-
recmap
reading and working with recombination maps in Rust
-
fusta
leverages the FUSE interface to transparently manipulate multiFASTA files as independent files
-
ross
A set of scripts to run basic analysis on fastq files
-
genomicsqlite
Genomics Extension for SQLite
-
mmap-bitvec
working with bit-vectors backed by memory-mapped files
-
to-trans
A high-performance transcriptome builder from fasta + GTF/GFF
-
guide-counter
Fast and accurate guide counting for CRISPR screens
-
primaldimer_rs
calculating PrimerPrimer interactions
-
gfastats
GFA statistics
-
libnail
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
-
kinesin
re-exports crate (WIP)
-
fastx
reads Fasta and FastQ files with little overhead
-
genome
package used to generate DNA used for GAN generator
-
spdi
format to describe a genomic variant. This crate provides a library to get an SPDI format representation of a variant and a command-line utility which adds SPDI format output to an input VCF file.
-
blobtk
Core utilities for BlobToolKit
-
psychophysics
psychophysical experiments
-
census2csv
Convert TMT multiplexed proteomics data in the Census format to CSV files
-
freesasa-sys
Rust raw FFI bindings for the freesasa C library
-
omics-variation
Foundational representations of variation in the Rust omics ecosystem
-
granges
command line tool for genomic range operations
-
genotype
An abstraction layer between genotype and phenotype, with in-place mutation
-
gia
set theoretic operations of genomic intervals
-
libparasail-sys
Unsafe Rust bindings for the parasail C library
-
chiral-common
Common Stuff of Chiral: An All-in-One Data Processing Tool
-
kractor
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
-
chainfile
working with genomics chain files
-
sorensen
Sørensen–Dice coefficient implementation for Rust
-
grass-runtime
Runtime library for GRASS
-
biostats
A bioinformatics library
-
fasta_windows
Make quick statistics in windows from a fasta file
-
lorikeet-rs
Strain resolver for metagenomics
-
libradicl
support library for alevin-fry
-
bedblocks
Split a BED file into blocks
-
wdl-grammar
A parse tree for Workflow Description Language (WDL) documents
-
sigalign-utils
utils for core
-
gkl
Genomics Kernel Library
-
consprob
Quick Probability Inference Engine on RNA Structural Alignment
-
minimap2-sys
Bindings to libminimap2
-
protein-translate
Translate nucleotide sequence to protein
-
genotype_visitor
Genotype language visitor crate
-
minced-parser
A parser for the output of the MinCED CRISPR array annotation tool
-
abpoa-sys
Automatically generated FFI definitions for abPOA
-
strif
identify interruptions in short tandem repeats across the genome
-
omnitigs
Omnitig-related algorithms
-
rosalind-cli
CLI for
rosalindcrate -
phenotype-internal
Defines
Phenotypetrait forPeapodcrate -
rumi
PCR Deduplication via directional adjacency
-
classeq-core
Core library for the classeq project
-
bio-rust
解析生物信息领域的基本数据结构，提供操纵这些数据的接口和构建一些统计模型。
-
exon-sam
Exon SAM
-
unitig_flipper
Reorienting unitigs to reduce the number of dummy nodes in an SBWT
-
sfs-cli
Tools for working with site frequency spectra
-
bigsig
Large-scale Sequence Search with BItsliced Genomic Signature Index (BIGSIG)
-
biosignal
processing biological signals
-
saboten
biedged graphs, cactus graphs and trees, and an algorithm for finding ultrabubbles in variation graphs
-
fg-stitch-lib
Stitch aligner implementation and supporting utilities
-
lightmotif-tfmpvalue
Rust reimplementation of TFMPvalue for the lightmotif crate
-
protein
Working with protein structures
-
nucleic-acids
creating DNA and RNA sequences
-
fastix
prefix renaming FASTA records
-
protein_translation
translate &str or String of RNA sequence with nucleotide into a Vec<&str> of their appropriate protein names
-
chaintools
Serialize and work with .chain files in Rust
-
exon-io
IO utilities for Exon
-
ngs
Command line tool for processing next-generation sequencing data
-
phcue-ck
command line tool to obtain FTP links to FASTQ files from ENA using run accession
-
radtk
A toolkit for working with RAD files
-
rust-spoa
wraps the C++ SPOA library for generating DNA and protein consensus sequences
-
grass-ir
IR for GRASS
-
noodles-refget
A refget client
-
rust-parallelfastx
Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does
-
pipspeak
converting PIPSeq files to 10X Genomics compatible FASTQ files
-
cgt_bacpop
Label core and rare genes in pangenome dataa
-
fq-filter-reads
program to filter a fastq file with a provided list of IDs
-
bam-builder
easily building BAMs for testing
-
genotype_lang_py_converter
Genotype language Python target converter crate
-
mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
-
libprosic
calling of genomic variants using a latent variable model
-
acetylene_parser
A parser for chemical formulas
-
fastx-statistics
Compute simple statistics for fasta-like files
-
demes-forward-capi
C API to demes-forward crate
-
pilercr-parser
A parser for the output of the PILER-CR CRISPR array annotation tool
-
aa-regex
macros to build regular expression matching protein sequences
-
ncbi
Rust data structures for NCBI APIs
-
alpine-core
ALPINE (Anachronistic Lineage and Persistent INfection Explorer) Core Utilities
-
piscem-infer
A flexible tool to perform target quantification from bulk-sequencing data
-
miniprot-sys
Bindings to libminiprot
-
exon-common
Common utilities for Exon
-
wham
weighted histogram analysis method
-
molcv
that calculates the circular variance of protein residues
-
gfacut
Cutting out parts of the genome
-
fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
-
crispr_helloworld
Hello world project
-
phylo
An extensible Phylogenetics library written in rust
-
read-structure
parsing and working with read structure descriptions
-
pedigree
Build a pedigree from WGS data
-
vcfverifier
Verifies that a given VCF matches a given FASTA by comparing the REF column in the VCF to the underlying FASTA sequences
-
drprg
Drug resistance prediction with reference graphs
-
multi-seq-align
Manipulate multiple sequence alignments (DNA/protein)
-
intc
*-INC method to calculate an empirical FDR for non-targeting controls in CRISPR screens
-
kgst
containing the implementation of a K-Truncated Generalized Suffix Tree using Ukkonen's Algorithm
-
nale
that performs profile Hidden Markov Model (PHMM) biological sequence alignment
-
consprob-trained
Trainable Probability Inference Engine on RNA Structural Alignment
-
candentia
A cli tool for managing CT-Scan data to study evolutionary biology
-
seqsplitter
Parses fasta records based on list of either header names or regexes
-
bam2seq
Extract reads and reconstructed references from a .bam file using CIGAR and MD tags
-
elm
A minimalist framework for Extreme Learning Machines (ELMs)
-
grafen
Create graphene and other substrates for use in molecular dynamics simulations
-
alphabeta
Tools for analysing epigenetic data
-
fffx
fasta/q/x file format parser. Well fuzzed.
-
fastxgz
A fasta/fastq parser for both compressed and not compressed files
-
aa-name
Basic enum for amino acid names
-
aa_similarity
Substitution matrices for use in protein sequence analysis and alignment
-
vcf
VCF Parser
-
bio
A bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields.
-
mfqe
FASTA/Q read extractor
-
crispr
designing sgRNAs for genome engineering using CRISPR/Cas9
-
rust-seq2kminmers
Construction and iteration of k-min-mers from a DNA sequence
-
classeq-ports-lib
A base library to share elements between Classeq ports
-
chiral-computing-unit
Computing Units of Chiral: An All-in-One Data Processing Tool
-
thirdkind
Read phylogenetic tree(s) in newick, phyloXML or recPhyloXML file and build a svg representation of the tree(s) allowing 1, 2 or 3 reconciliation levels
-
stats_on_genomes
Calculate 2 simple ratio on the whole genome: GC ratio and repetition ratio
-
jean
Computational biology utility library for Rust featuring sequence alignment, genome annotation, and I/O of biological files
-
readfish-tools
Tools for analysing adaptive sampling data
-
sdust
symmetric DUST algorithm, with optional CLI
-
select-random-fastx
Select random entries from fastx files
-
genotype_lang_py_tree
Genotype language Python target AST crate
-
libwfa
Bindings to the C implementation of the WFA alignment algorithm
-
readmerger
rapidly merging FASTQ files. Never use cat again!
-
phantompurger-rs
Detecting chimeric molecules in scRNAseq
-
seqsample
Randomly sample sequences from a FASTA file
-
rboss
Rust Bioinformatics Toolbox
-
handlegraph
in variation graphs
-
ukhs
Universal K-mer Hitting Sets
-
krakenxtract
Extract reads from a FASTQ file based on taxonomic classification via Kraken2
-
crast
Context RNA Alignment Search Tool
-
exon-bcf
Exon BCF
-
rna-algos
RNA Bioinformatics Algorithms
-
jean_blosum
BLOSUM feature for jean
-
metaprofile
Segregate WGS data into windows along the genome. Optionally, run tools such as alphabeta for each window.
-
alpaca
caller for genomic variants (single nucleotide and small indels) from next-generation sequencing data that uses a novel algebraic approach to incorporate sample based filtering into the calling…
-
skc
Shared k-mer content between two genomes
-
blastdb-sequence-util
encoding nucleotide/protein sequences in BLAST database format
-
sce
importing and managing various single-cell matrices