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Search results for fasta fastq

104 search results found

Oneliners ⭐ 1,705

Useful bash one-liners for bioinformatics.

Seqtk ⭐ 1,148

Toolkit for processing sequences in FASTA/Q formats

Seqkit ⭐ 1,133

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Bioinformatics One Liners ⭐ 277

Bioinformatics one liners from Ming Tang

Krakentools ⭐ 242

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Randomly subsample sequencing reads to a specified coverage

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Genozip ⭐ 144

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

Fastx_toolkit ⭐ 109

FASTA/FASTQ pre-processing programs

Fast multi-line FASTA/Q reader in several programming languages

Isoquant ⭐ 98

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

🚀 seqfu - Sequece Fastx Utilities

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

A DNA Sequence Alignment/Map (SAM) library for Clojure

Mcclintock ⭐ 83

Meta-pipeline to identify transposable element insertions using next generation sequencing data

Phylosift ⭐ 68

Phylogenetic and taxonomic analysis for genomes and metagenomes

Opengene.jl ⭐ 61

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

FASTA and FASTQ parsing in Rust

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

Efficiently read and write sequencing data from Python

Metacache ⭐ 49

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

Fastx.jl ⭐ 48

Parse and process FASTA and FASTQ formatted files of biological sequences.

A genomics-proteomics toolkit

Python3 scripts to manipulate FASTA and FASTQ files

PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

Frequently used commands in bioinformatics

Fasta_utilities ⭐ 37

A collection of scripts developed to interact with fasta, fastq and sam/bam files.

Antonie is an integrated, robust, reliable and fast processor of DNA reads

Deep learning library for biological sequences. Extension of Fastai and Pytorch.

Utility program for extracting sequences from a fasta/fastq file

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

Blast2bam ⭐ 33

Blast2Bam uses the XML results of Blastn, the reference and the fastQ or fasta file(s) to output a SAM file.

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

Bioawk Tutorial ⭐ 30

Bioinf Commons ⭐ 30

Bioinformatics library in Kotlin

Bam2fastx ⭐ 28

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.

Readability enhancement tool for bioinformatics data file format

Fastascripts ⭐ 26

Manipulate FASTA files

Demultiplex ⭐ 26

Versatile FASTA/FASTQ demultiplexer.

FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation

Fast and flexible ORF finder

An approximate sequence pattern matcher for FASTQ/FASTA files.

Soap3 Dp ⭐ 24

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously.

This repository is deprecated, please use the link to the right.

Fusiondirect.jl ⭐ 23

(No maintenance) Detect gene fusion directly from raw fastq files

Biohansel ⭐ 21

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

Assembler Components ⭐ 20

Components of genome sequence assembly tools

Various bioinformatics tools

DuckDB Extension for reading and writing FASTA and FASTQ Files

Sync paired-end FASTA/Q files and keep singleton reads

Reads For Assembly ⭐ 17

Simulate metagenomic short reads from one or more populations.

Rabbitmash ⭐ 16

RabbitMash: an efficient highly optimized implementation of Mash.

Kmer2snp ⭐ 16

Fast and Accurate Classification of Sequences using Bloom filters

A FASTA/FASTQ format parser library

Accurate and fast taxonomic classification using pseudoaligning

Fast and flexible tool for reading, modifying and writing biological sequences

Nimreadfq ⭐ 15

A wrapper to Heng Li's kseq/readfq, an efficient FastQ/Fasta parser

Ngs Protocols ⭐ 15

Scripts to run several protocols to process and analyze Next-Generation Sequencing data

Miscperlscripts ⭐ 15

Small collection of random useful perl scripts

Enasearch ⭐ 15

A Python library for interacting with ENA's API

Kontaminant ⭐ 14

Tool to look for contaminants, with a kmer database.

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

De novo adapter prediction algorithm for small RNA sequencing data

Simple and quick FastQ and FastA tool for file reading and conversion

A collection of command-line tools I wrote to make various repetitive tasks more convenient

Comparing and combining multiple metagenomic datasets

Microbiome Classifier Pipeline for Pacific Biosciences 16s Data

Sequencing_for_genetics ⭐ 11

유전학자를 위한 시퀀싱 자료 분석

Sequence Database Curator ⭐ 10

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Eqp Cluster ⭐ 10

Unix-based RNA-seq quantification pipeline

Bioruby Faster ⭐ 9

A fast and simple parser for Fasta / FastQ files

Lightweight C++ library for reading FASTA and FASTQ files.

Seq Collection ⭐ 9

Fastq_generator ⭐ 9

A suite of tools to generate random or mapped fastq files

Biocpp Io ⭐ 8

BioC++ Input/Output library

Metacrast ⭐ 8

MetaCRAST: reference-guided CRISPR detection in metagenomes

Library for Reading Bioinformatic Sequence Data in C

Toolkit for manipulating FASTA and SAM files

A random collection of kotlin utilities

Fastx_read_count ⭐ 7

Tiny program to count reads in FASTA/FASTQ files

4 Rna Seq ⭐ 7

A slurm based pipeline for RNA-seq analysis to execute on linux clusters. Feel free to connect to visualize your RNA-seq data on the clouds

Looking for mutations in PacBio cancer data: an alignment-free method

Seqfilter ⭐ 7

Versatile FASTA/FASTQ sequence file analysis and modification tool

Fast tool for sequence related tasks

LAVA: Longitudinal Analysis of Viral Alleles

Pipeline for CnR, CnT

Fastqsifter ⭐ 6

Separate contaminating reads from FASTQ files (e.g., mitochondria, symbionts, bacterial or human contaminants)

egaz and alignDB work with external (NCBI/EBI) data

CAARS: Comparative Assembly and Annotation of RNA-Seq data

TE tools for TE RNASeq and smallRNASeq analysis with galaxy

FASTA/FASTQ alignment

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