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Search results for fasta

639 search results found

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

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

A Go package for engineering organisms.

Vsearch ⭐ 605

Versatile open-source tool for microbiome analysis

BWK awk modified for biological data

Biotite ⭐ 515

A comprehensive library for computational molecular biology

Jupyter Renderers ⭐ 478

Renderers and renderer extensions for JupyterLab

SeqAn's official repository.

Pyfaidx ⭐ 427

Efficient pythonic random access to fasta subsequences

⚡ ♒ Rapid prokaryotic genome annotation

✂️ ⚡ Rapid haploid variant calling and core genome alignment

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

Minigraph ⭐ 367

Proof-of-concept seq-to-graph mapper and graph generator

Gffread ⭐ 288

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

Bioinformatics One Liners ⭐ 277

Bioinformatics one liners from Ming Tang

A Java API for high-throughput sequencing data (HTS) formats.

Interproscan ⭐ 259

Krakentools ⭐ 242

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

Cdna_cupcake ⭐ 224

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

Vcf2phylip ⭐ 216

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Pyfastx ⭐ 211

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

Variational autoencoder for metagenomic binning

JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis.

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/g Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

a JavaScript DNA, RNA, and protein sequence viewer

Biosyntax ⭐ 184

Syntax highlighting for computational biology

Gfatools ⭐ 181

Tools for manipulating sequence graphs in the GFA and rGFA formats

Gtotree ⭐ 174

A user-friendly workflow for phylogenomics

Aligngraph ⭐ 165

Algorithm for secondary de novo genome assembly guided by closely related references

Randomly subsample sequencing reads to a specified coverage

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Reference-guided transcript discovery and quantification for long read RNA-Seq data

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

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Novoplasty ⭐ 140

NOVOPlasty - The organelle assembler and heteroplasmy caller

🆔 Scan contig files against PubMLST typing schemes

A minimap2 frontend for PacBio native data formats

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

Vcf Validator ⭐ 125

Validation suite for Variant Call Format (VCF) files, implemented using C++11

Badread ⭐ 124

a long read simulator that can imitate many types of read problems

Das_tool ⭐ 124

Boosting RNA-Seq assemblies with partial or related genomic sequences

Redundans ⭐ 121

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Mirdeep2 ⭐ 120

Discovering known and novel miRNAs from small RNA sequencing data

A basecaller for Oxford Nanopore Technologies' sequencers

Sibeliaz ⭐ 113

A fast whole-genome aligner based on de Bruijn graphs

A robust and fast clustering method for amplicon-based studies

Fastx_toolkit ⭐ 109

FASTA/FASTQ pre-processing programs

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

Dna2vec ⭐ 103

dna2vec: Consistent vector representations of variable-length k-mers

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Single unified API for all DBOpenData APIs implemented with GraphQL.

SKESA assembler

Get_homologues ⭐ 98

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

Isoquant ⭐ 98

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

🚀 seqfu - Sequece Fastx Utilities

Git repository for FASTA36 sequence comparison software

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

compacted de Bruijn graph construction in low memory

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

Mcclintock ⭐ 83

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

Deblur is a greedy deconvolution algorithm based on known read error profiles.

Scrappie ⭐ 81

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group

Mummer2circos ⭐ 79

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

Biobambam2 ⭐ 79

Tools for early stage alignment file processing

fast, memory-efficient, pythonic (and command-line) access to fasta sequence files

Polyester ⭐ 76

Bioconductor package "polyester", devel version. RNA-seq read simulator.

Python package and CLI for whole-genome duplication related analyses

Biobloom ⭐ 70

Create Bloom filters for a given reference and then use it to categorize sequences

Clj Biosequence ⭐ 70

A Clojure library designed to make the manipulation of biological sequence data easier.

Phylosift ⭐ 68

Phylogenetic and taxonomic analysis for genomes and metagenomes

Snp Dists ⭐ 68

Pairwise SNP distance matrix from a FASTA sequence alignment

Phased assembly variant caller

Fast fusion detection using kallisto

Haplogrep Cmd ⭐ 64

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.

Cas Offinder ⭐ 63

An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.

GenMap - Fast and Exact Computation of Genome Mappability

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

A hybrid assembly and MAG recovery pipeline (and more!)

Opengene.jl ⭐ 61

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

Plasflow ⭐ 61

Software for prediction of plasmid sequences in metagenomic assemblies

FASTA and FASTQ parsing in Rust

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

flexible barcode and adapter removal

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

Conterminator ⭐ 57

Detection of incorrectly labeled sequences across kingdoms

Emblmygff3 ⭐ 57

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

Flexidot ⭐ 56

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

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.

Orthomcl Pipeline ⭐ 55

Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0

TIDDIT - structural variant calling

Jupiterplot ⭐ 54

A Circos-based tool to visualize genome assembly consistency

Transanno ⭐ 54

accurate LiftOver tool for new genome assemblies

Fastahack ⭐ 54

utilities for indexing and sequence extraction from FASTA files

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