Lib.rs

› Keywords #bioinformatics #fasta #genomics #bio #k-mer #sequencing #fasta-sequence

#fastq

  1. needletail

    FASTX parsing and k-mer methods

    v0.6.3 9.8K #bioinformatics #fasta #k-mer #fastq

  2. minimap2

    Bindings to libminimap2

    v0.1.30+minimap2.2.30 600 #genomics #bioinformatics #fasta #fastq

  3. seq_io

    Fast FASTA, FASTQ and FASTX parsing

    v0.4.0-alpha.0 3.0K #fastq #fasta #bio

  4. rasusa

    Randomly subsample reads or alignments

    v2.2.2 750 #bioinformatics #fastq #coverage #subsampling #alignment

  5. fqkit

    cross-platform program for fastq file manipulation

    v0.4.14 3.3K #bio #fastq #hts #barcode

  6. paraseq

    A minimal-copy parser for FASTA and FASTQ files built for paired parallel processing

    v0.4.8 1.0K #fastq #fasta #parser

  7. merkurio

    Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags

    v1.0.2 #k-mer #sam #fasta #fastq #bio

  8. grepq

    quickly filter fastq files

    v1.6.5 3.4K #bioinformatics #fastq #json

  9. kira-qc

    FastQC-compatible QC tool written in Rust

    v0.1.0 #genomics #bioinformatics #fastq #quality-control #dna

  10. hashfasta

    Very quickly compute hashes for FASTA/FASTQ files considering only the sequence content

    v1.0.0 #bioinformatics #fasta #hash #fastq #sequencing

  11. primerpincer

    A CLI primer trimming tool for long-read sequencing data

    v0.8.0 #bioinformatics #sequencing #fastq #primers #microbiome

  12. kractor

    Extract reads from a FASTQ file based on taxonomic classification via Kraken2

    v4.0.0 #bioinformatics #fastq #metagenomics #taxonomy #kraken

  13. fastx

    reads Fasta and FastQ files with little overhead

    v0.6.1 #bioinformatics #fasta #fastq #sequencing #genome

  14. seqsizzle

    A pager for viewing FASTQ and FASTA files with fuzzy matching, allowing different adaptors to be colored differently

    v0.4.1 #bioinformatics #fastq #pager #visualization #genomic-sequencing

  15. minimap2-temp

    Bindings to libminimap2

    v0.1.33+minimap2.2.28 190 #bioinformatics #fasta #fastq

  16. rust-bio-tools

    A set of fast and robust command line utilities for bioinformatics tasks based on Rust-Bio

    v0.42.2 4.1K #bioinformatics #genomics #bam #fastq #rust-bio #fuzzy-matching #csv #html-reports #bcf #plot

  17. fasten

    A set of scripts to run basic analysis on fastq files

    v0.9.0 #bioinformatics #fastq #streaming

  18. seqtkrs

    reimplementation of seqtk, a fast and lightweight tool for processing biological sequences in FASTA/FASTQ format

    v0.1.1 #genomics #fasta-sequence #bioinformatics #bioinformatics-sequence #fasta #fastq

  19. fastq-fix-i5

    Rewrite FASTQ headers by reverse-complementing only the i5 (P5/index2) part in ...:i7+i5

    v1.0.0 #fastq #bioinformatics #sequencing

  20. fastars

    Ultra-fast QC and trimming for short and long reads

    v0.1.0 #bioinformatics #trimming #qc #fastq #ngs

  21. binseq

    A high efficiency binary format for sequencing data

    v0.9.0 #genomics-sequencing #genomics #sequencing #fastq #bio #nucleotide

  22. fasterp

    High-performance FASTQ preprocessing tool - often faster than fastp with the same interface

    v0.2.1 #genomics #bioinformatics #quality-control #fastq

  23. mbf-fastq-processor

    The fast, reliable multitool of FASTQ processing

    v0.8.1 #bioinformatics #fastq #sequencing

  24. seq_io_parallel

    A map-reduce style parallel extension to seq_io

    v0.2.1 700 #bioinformatics #fastq #map-reduce #fasta

  25. back_to_sequences

    Back to sequences: find the origin of kmers

    v0.8.3 #k-mer #fasta #find #back #fastq #multi-line #gz #percentage #maximal

  26. filterx

    A command line tool to filter data by using python-like syntax

    v0.4.1 750 #sam #csv #filter #fastq #fasta #gff #tsv #bed #command-line-tool #python-like

  27. selexqc

    High-performance parallel RNA Capture-SELEX library quality control

    v0.1.0 #bioinformatics #fasta-sequence #bioinformatics-sequence #fasta #fastq #selex

  28. minimap2-sys

    Bindings to libminimap2

    v0.1.30+minimap2.2.30 700 #bioinformatics #fasta #fastq

  29. bamslice

    Extract byte ranges from BAM files and convert to interleaved FASTQ format for parallel processing

    v0.1.7 #bam #genomics #bioinformatics #fastq

  30. fastqc-rs

    A fast quality control tool for FASTQ files written in rust

    v0.3.4 460 #fastq #quality-control #sequence-quality

  31. nucleaze

    Read filtering using k-mers

    v1.4.0 #k-mer #reference #fasta #filtering #matching #input-file #serialization #bioinformatics #brian #fastq

  32. fqgrep

    Search a pair of fastq files for reads that match a given ref or alt sequence

    v1.1.1 160 #genomics #bioinformatics #fastq

  33. jseqio

    Reading and writing biological sequences in FASTA or FASTQ format

    v0.1.6 #fasta-sequence #fastq #format #stream #iterator #compression

  34. grz-check

    validating incoming files of Modellvorhaben §64e submissions to Genomrechenzentren (GRZ) in Germany

    v0.2.1 #fastq #validation #submission #fixed-length #jsonl #bam-file #integrity-checks #germany #progress-bar #sha-256

  35. prseq

    Rust tools (with Python bindings) for sequence analysis

    v0.0.33 #bioinformatics #sequence-analysis #fastq #fasta

  36. fastqgen

    Random paired fastq file generation. Nothing more, nothing less.

    v0.1.4 #bioinformatics #fastq #generate

  37. seqtable

    High-performance parallel FASTA/FASTQ sequence counter

    v0.1.1 #bioinformatics #fasta-sequence #fastq #fasta #parquet #bioinformatics-sequence

  38. noodles-fastq

    FASTQ format reader and writer

    v0.21.0 4.5K #fastq #reader-writer #bio

  39. kira_cdh_compat_fastq_reader

    Streaming FASTQ reader compatible with CD-HIT input handling (plain and .gz), safe idiomatic Rust API; sync and async

    v0.1.3 #fastq #bioinformatics #gzip #streaming #cd-hit

  40. matchbox-cli

    A flexible processor for sequencing reads

    v0.3.1 #sequencing #fasta #fastq #bam #processor #edit-distance #mb #fq

  41. flash-cli

    Command-line interface for the FLASH read merging algorithm

    v0.1.0 #bioinformatics #fastq #cli

  42. gskits

    common kits

    v0.15.15 #kit #file-reader #fasta-vcf #bed #reverse-complement #fastq #bam #samtools #dna #pbar

  43. kseq

    fasta/fastq format parser library

    v0.5.3 #fastq #fasta

  44. barcode-count

    NGS barcode counter for DEL, CRISPR-seq, and Barcode-seq

    v0.11.1 #barcode-seq #next-generation-sequencing #fastq #del #counter #crispr-sequencing #data-analysis #quality-score #dna #format-file

  45. kira_cdh_compat_kmer_indexer

    CD-HIT-compatible k-mer indexing (CD-HIT-NG) in Rust: fast, memory-efficient, mmap-ready

    v0.2.0 #bioinformatics #k-mer #fastq #cd-hit #index

  46. fastq

    A parser for fastq

    v0.6.0 200 #bio #parser

  47. seq-events

    A minimal, zero-copy streaming parser for FASTA/FASTQ files

    v0.1.0 #bioinformatics #streaming-parser #fastq #fasta

  48. fastlin

    an ultra-fast program for MTBC lineage typing

    v0.4.1 170 #fastq #bam #lineage #fasta #typing

  49. ontime

    Extract subsets of ONT (Nanopore) reads based on time

    v0.3.1 #bioinformatics #nanopore #fastq #time

  50. filterx_info

    The builtin function documentation library for filterx

    v0.4.1 410 #filterx #sam #documentation #fastq #fasta #tsv #gff #bed #bioinformatics #csv

  51. deepbiop-fq

    Deep Learning Preprocessing Library for Fastq Format

    v0.1.16 #deep-learning #parquet #fastq

  52. filterx_source

    The source library for filterx

    v0.4.1 500 #filterx #fastq #fasta #fasta-vcf #sam #bed #tsv #gff #csv #bioinformatics

  53. filterx_engine

    The engine library for filterx

    v0.4.1 500 #filterx #fastq #sam #fasta #vcf #tsv #gff #bed #csv #bioinformatics

  54. isONclust3

    novel de novo clustering algorithm. isONclust3 is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene family…

    v0.3.0 230 #isonclust3 #cluster-analysis #fastq #long-read #read-file #tsv #nanopore #gene #per-file #oxford #came

  55. seqtk-rs

    sequence processing tool written in Rust for manipulating FASTA/FASTQ files. Pure rust version of seqtk.

    v0.2.0 #bio #fasta-sequence #fasta #fastq #ngs

  56. flash-lib

    Rust port of the FLASH read merging algorithm

    v0.1.0 #bioinformatics #flash #fastq

  57. exon-fastq

    FASTQ support for Exon

    v0.32.4 #bioinformatics #exon #fastq #proteomics #arrow #sql #query-engine

  58. fastleng

    read length statistics tool

    v0.2.0 #length #statistics #fastq #fasta #generator #fastx #metrics #fastx-file #n50 #bam-file

  59. bio-streams

    Streaming bioinformatics data types

    v0.5.0 130 #genomics #bioinformatics #fastq #fasta

  60. spikeq

    A synthetic FASTQ record generator with pattern spiking

    v1.0.1 120 #bioinformatics #fastq #spike

  61. bio-jtools

    A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data

    v0.2.0 #bioinformatics #fastq #cli

  62. bamsalvage

    Rust version of bamsalvage, retrieving sequences from a corrupted BAM file as much as possible

    v0.1.3 #bio #long-read #fastq #fasta

  63. biotest

    Generate random test data for bioinformatics

    v0.2.0 #bioinformatics #random #random-test #random-data #fastq #random-sequence #testing-data #fasta

    64. Try searching with DuckDuckGo.

  64. fastxgz

    A fasta/fastq parser for both compressed and not compressed files

    v0.4.0 #fastq #fasta #compression #gz #k-mer #fastx #hash

  65. ross

    A set of scripts to run basic analysis on fastq files

    v0.1.7 #bioinformatics #fastq #friends

  66. seqdupes

    Compress sequence duplicates

    v0.2.0 #fasta #fastq

  67. fastq-generator

    A fastq generator for generation of synthetic fastq files

    v0.1.1 #bioinformatics #random #fastq

  68. filterx_core

    The core library for filterx

    v0.4.1 500 #csv #sam #fastq #fasta #tsv #gff #bed

  69. rust-parallelfastx

    Parallel iteration of FASTA/FASTQ files, for when sequence order doesn't matter but speed does

    v0.1.1 #bioinformatics #fastq #fasta

  70. fastx-statistics

    Compute simple statistics for fasta-like files

    v1.0.0 #statistics #compute #fasta #fastq

  71. seqio

    File reading and writing, support gzip format compression

    v0.1.1 #gzip #compression #format #fastq #read-file

  72. fffx

    fasta/q/x file format parser. Well fuzzed.

    v0.1.3 240 #bioinformatics #fastq #fasta #compression

  73. fq-filter-reads

    program to filter a fastq file with a provided list of IDs

    v0.1.1 #fastq #list #record #testing #id

  74. 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。

    v0.1.1 #fastq #parser

  75. lrdf

    Commandline tool to generate a dataframe from Oxford Nanopore FastQ

    v0.2.0 #dataframe #fastq #nanopore #tsv #command-line

  76. krakenuniq-rs

    port of krakenuniq

    v0.0.4 950 #k-mer #fastq #port

  77. syncmers

    finding syncmers

    v0.1.5 #bioinformatics #bioinformatics-sequence #fasta #fastq #fasta-sequence

  78. select-random-fastx

    Select random entries from fastx files

    v0.1.1 #fasta #fastq #entries #fastx #random

  79. phcue-ck

    command line tool to obtain FTP links to FASTQ files from ENA using run accession

    v0.2.0 #bioinformatics #fastq

  80. vbinseq

    A high efficiency binary format for sequencing data with variable-length records

    v0.1.7 150 #genomics #genomics-sequencing #bioinformatics #fastq #sequencing #nucleotide

  81. rustfastq

    bare metal fastq parsing

    v0.5.0 #bioinformatics #fastq

  82. seqsample

    Randomly sample sequences from a FASTA file

    v0.2.0 #fasta #fasta-sequence #fastq

  83. seqsplitter

    Parses fasta records based on list of either header names or regexes

    v0.1.4 #fastq #fasta

  84. mfqe

    FASTA/Q read extractor

    v0.5.0 #fasta #fastq #extractor #name #set

  85. seqcomplexity

    Calculates per-read and total sequence complexity from FastQ file

    v0.1.2 #fastq