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needletail
FASTX parsing and k-mer methods
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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.
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rust-htslib
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files
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finch
An implementation of min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
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rust-lapper
A fast and easy interval overlap library
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finch_cli
An implementation of min-wise independent permutation locality sensitive hashing ('MinHashing') for genomic data and command-line utility for manipulation
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crispr_screen
A fast and configurable differential expression analysis tool for CRISPR screens
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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
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rust-bio-tools
A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio
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alignoth
A tool for creating alignment plots from bam files
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alevin-fry
A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data
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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
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noodles
Bioinformatics I/O libraries
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atg
Convert transcripts between different file formats
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sfasta
Better FASTA sequence compression and querying
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nucleob
bioinformatics: nucleobases and amino acids statistics
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consprob
Quick Probability Inference Engine on RNA Structural Alignment
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genevo
genevo provides building blocks to run simulations of optimization and search problems using genetic algorithms (GA). Execute genetic algorithm (GA) simulations in a customizable and extensible way
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gsearch
genome classification, probminhash hnsw, genome search
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rasusa
Randomly subsample reads to a specified coverage
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bio-seq
Bit packed and well-typed biological sequences
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rnapkin
CLI utility for drawing RNA secondary structure
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intspan
Command line tools for IntSpan related bioinformatics operations
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lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices
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fastax
Make phylogenetic trees and lineages from the NCBI Taxonomy database
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pdbtbx
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files
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fqkit
fqkit: a simple program for fastq file manipulation
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light_phylogeny
Methods and functions for phylogeny
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genome-graph
Representation of genome graphs
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nwbview
Neurodata Without Borders viewer
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seal
Implementation of Needleman-Wunsch & Smith-Waterman sequence alignment
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bed-reader
Read and write the PLINK BED format, simply and efficiently
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simpleaf
A rust framework to make using alevin-fry even simpler
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sigalign
Pairwise alignment algorithm using gap-affine penalty for nucleotide and amino-acid sequences
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skani
skani is a 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…
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noodles-csi
Coordinate-sorted index (CSI) format reader and writer
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verify-same-kmer-content
Verify that an SPSS has the same kmer content as a set of unitigs
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genomicsqlite
Genomics Extension for SQLite
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vcf
VCF Parser
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coprosize
coprolite research (paleontology and archaeology): estimate the producer's body mass based on coprolite diameter by the use of regression models
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minimap2
Bindings to libminimap2
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hgvs
Port of biocommons/hgvs to Rust
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phylotree
A crate to deal with phylogenetic trees and distance matrices
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taxonomy
Routines for loading, saving, and manipulating taxonomic trees
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slow5
Library for interacting with slow5
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fmlrc
FM-index Long Read Corrector - Rust implementation
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perbase
Fast and correct perbase BAM/CRAM analysis
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fasten
A set of scripts to run basic analysis on fastq files
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lipmaa-link
A function to calculate lipmaa sequence numbers
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varlociraptor
A library for calling of genomic variants using a latent variable model
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consalifold
Consensus Secondary Structure Predictor Engaging Structural Alignment-based Error Correction
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nwr
nwris a command line tool for newick and taxonomy -
mehari
Variant effect prediction all in Rust
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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
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fasta_tools
Some tools that are 'internal' for now because they are insufficiently refined and unstable, but which are used by other 'public' crates
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ska
Split k-mer analysis
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fqtk
A toolkit for working with FASTQ files
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uniprot
Rust data structures and parser for the Uniprot database(s)
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gfa
Library for working with graphs in the GFA (Graphical Fragment Assembly) format
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ontime
Extract subsets of ONT (Nanopore) reads based on time
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nale
Nale is a library that performs profile Hidden Markov Model (PHMM) biological sequence alignment
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blobtk
Core utilities for BlobToolKit
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lightmotif-py
PyO3 bindings and Python interface to the lightmotif crate
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librna-sys
Low-level bindings for the ViennaRNA library
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gchemol
gchemol: a Graph-based CHEMical Objects Library
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varfish-server-worker
Rust-based workers for varfish-server
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bio-jtools
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data
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fxtools
A collection of commandline Fasta/Fastq utility tools
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protein_translation
A crate to translate &str or String of RNA sequence with nucleotide into a Vec<&str> of their appropriate protein names
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stats_on_gff3
Calculate statistics such as CDS GC3 ratio, intron GC ratio, flanking gene region GC ratio, first intron length, number of introns
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chiral-common
Common Stuff of Chiral: An All-in-One Data Processing Tool
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ncbitaxonomy
Read NCBI Taxonomy Database from files and work with NCBI Taxonomy DB
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bird_tool_utils
Microbial genomics utility functions
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fastx-statistics
Compute simple statistics for fasta-like files
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read-structure
Library for parsing and working with read structure descriptions
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distance_aa
A backend for the distAAnce web application
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noodles-fasta
FASTA format reader and writer
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compact-genome
Representation of genomes
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yacrd
Using all-against-all read mapping, yacrd performs: computation of pile-up coverage for each read and detection of chimeras
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pilercr-parser
A parser for the output of the PILER-CR CRISPR array annotation tool
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entrez-rs
Rust wrapper for the Entrez API
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fastx
FastX reads Fasta and FastQ files with little overhead
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nthash
ntHash is a rolling hash function for hashing all possible k-mers in a DNA sequence
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fusta
FUSTA leverages the FUSE interface to transparently manipulate multiFASTA files as independent files
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fastq
A parser for fastq
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census2csv
Convert TMT multiplexed proteomics data in the Census format to CSV files
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noodles-tabix
Tabix (TBI) format reader and writer
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bamrescue
Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them
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gb-io
A library for parsing, writing and manipulating Genbank sequence files
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hts
Rust binding for htslib
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casgen
A way to generate cas12 6-plex CRISPR sequences
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fastleng
fastleng - read length statistics tool
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libradicl
support library for alevin-fry
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bioutils
Utilities and alphabets for biological sequence data
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seqsample
Randomly sample sequences from a FASTA file
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lib3dmol
Lib3dmol is a library written in rust to read, manipulate, select atoms in protein structure files
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fasta_windows
Make quick statistics in windows from a fasta file
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tables
Some tools that are 'internal' for now because they are insufficiently refined and unstable, but which are used by other 'public' crates
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freesasa-sys
Rust raw FFI bindings for the freesasa C library
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frag_gene_scan_rs
Rust implementation of the gene prediction model for short and error-prone reads
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nu_plugin_bio
Parse and manipulate common bioinformatic formats in nushell
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whittaker_map_generator
A map generator, generates biomed based on the Whittaker Diagram
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fq-filter-reads
This is a simple program to filter a fastq file with a provided list of IDs
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consprob-trained
Trainable Probability Inference Engine on RNA Structural Alignment
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blastdb-sequence-util
Utilities for encoding nucleotide/protein sequences in BLAST database format
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jean_blosum
BLOSUM feature for jean
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protein-translate
Translate nucleotide sequence to protein
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guide-counter
Fast and accurate guide counting for CRISPR screens
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atglib
A library to handle transcripts for genomics and transcriptomics
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ppgg
A library and an 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…
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fakit
fakit: a simple program for fasta file manipulation
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ggca
Computes efficiently the correlation (Pearson, Spearman or Kendall) and the p-value (two-sided) between all the pairs from two datasets
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minced-parser
A parser for the output of the MinCED CRISPR array annotation tool
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fpa_lr
fpa filter long read mapping information to save disk space
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biofile
A library for reading bioinformatics related files
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sourmash
MinHash sketches for genomic data
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bam2seq
Extract reads and reconstructed references from a .bam file using CIGAR and MD tags
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elias_fano_rust
An optimized implementation of Sebastiano Vigna's Elis-Fano quasi succint datastructure
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drprg
Drug resistance prediction with reference graphs
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bedrs
Genomic interval library in rust
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census-proteomics
Rust library for working with proteomics data quantified by the Census algorithm
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libsfasta
Better FASTA sequence compression and querying
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seqsplitter
Parses fasta records based on list of either header names or regexes
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chiral-data
Data Management Module of Chiral: An All-in-One Data Processing Tool
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xdrfile
Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format.
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gfastats
GFA statistics
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heme
PDB reader and other protein modeling tools
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vdj_types
Some tools that are 'internal' for now because they are insufficiently refined and unstable, but which are used by other 'public' crates
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multi-seq-align
Manipulate multiple sequence alignments (DNA/protein)
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select-random-fastx
Select random entries from fastx files
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smiles-parser
SMILES (chemical formula) parser based on the OpenSMILES spec
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gfautil
Command line tools for working with GFA files and related formats
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rust-spoa
This crate wraps the C++ SPOA library for generating DNA and protein consensus sequences
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sce
A library for importing and managing various single-cell matrices
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fqgrep
Search a pair of fastq files for reads that match a given ref or alt sequence
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pubchem
Rust data structures and client for the PubChem API
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chem-parse
A parser for simple chemical forumulas
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sgcount
A fast and flexible sgRNA counter
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weepingtown
Social psychology and sociology, individual and group behavior for my Hornvale project
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sid_vec
Tiny library providing id types and an id-based vector
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lorikeet-rs
Strain resolver for metagenomics
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rumi
PCR Deduplication via directional adjacency
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noodles-cram
CRAM format reader and writer
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jean_io
I/O library feature for jean
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mop-adapters
Solver adapters for MOP
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cramino
A tool to quickly extract quality metrics from bam or cram files
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protein
Working with protein structures
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omnitigs
Omnitig-related algorithms
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GetPDB
Download Protein files from rcsb.org
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ross
A set of scripts to run basic analysis on fastq files
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consalign
RNA Structural Aligner Based on Transfer-learning and Thermodynamic Ensemble Model
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rust-parallelfastx
Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does
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psdm
Compute a pairwise SNP distance matrix from one or two alignment(s)
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phcue-ck
phcue-ck is a command line tool to obtain FTP links to FASTQ files from ENA using run accession
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gfacut
Cutting out parts of the genome
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aa-regex
Utility macros to build regular expression matching protein sequences
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mudskipper
Convert genomic alignments to transcriptomic BAM/RAD files
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ggetrs
Efficient querying of biological databases from the command line
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rosalind-cli
CLI for
rosalindcrate -
phenotype-internal
Defines
Phenotypetrait forPeapodcrate -
biostats
A bioinformatics library
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crispr_helloworld
Hello world project
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hts-sys
This library provides HTSlib bindings
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biosignal
Library for processing biological signals
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cheminee
Molecule indexing and search
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slow5lib-sys
Low-level bindings to the slow5lib C library
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kmer-papa
Determine genes with significantly more mutations than expected by chance
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noodles-bed
BED (Browser Extensible Data) reader
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chiral-operator
Operators f Chiral: An All-in-One Data Processing Tool
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maelstrom-core
Tools for processing of NGS data
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scalc
A type that ensures calculation safety and prevents itself from overflow
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rna-ss-params
Library of RNA secondary structure parameters
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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。
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drug-extraction-core
A core library for extracting drugs from text records
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rust-seq2kminmers
Construction and iteration of k-min-mers from a DNA sequence
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casmap
A way to count and characterize constructs for cas12 6-plex CRISPR screens
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mmap-bitvec
A library for working with bit-vectors backed by memory-mapped files
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jean_cut
Codon usage tables feature for jean
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libprosic
A library for calling of genomic variants using a latent variable model
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fffx
Another fasta/q/x file format parser. Well fuzzed.
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rget_pdb
Download Protein files from rcsb.org
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nucleic-acids
A library for creating DNA and RNA sequences
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handlegraph
Library for use in variation graphs
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mmft
A minimal fasta toolkit
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genome
A simple package used to generate DNA used for GAN generator
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crispr
Rust library for designing sgRNAs for genome engineering using CRISPR/Cas9
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ukhs
Universal K-mer Hitting Sets
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ring_api
Strongly-typed client for the RING HTTP API
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aa-name
Basic enum for amino acid names
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variantkey
Pure rust implementation of variantkey
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noodles-fastq
FASTQ format reader and writer
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aa_similarity
Substitution matrices for use in protein sequence analysis and alignment
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minimap2-sys
Bindings to libminimap2
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kmer_lookup
Some tools that are 'internal' for now because they are insufficiently refined and unstable, but which are used by other 'public' crates
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fxread
A barebones fastx reader for rust
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jean_core
Core package of jean
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crast
CRAST, Context RNA Alignment Search Tool
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chiral-computing-unit
Computing Units of Chiral: An All-in-One Data Processing Tool
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seqdupes
Compress sequence duplicates
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rna-algos
Library of RNA Bioinformatics Algorithms