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Search results for bioinformatics fasta
bioinformatics
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fasta
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120 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
Poly
⭐
620
A Go package for engineering organisms.
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Bioawk
⭐
518
BWK awk modified for biological data
Biotite
⭐
515
A comprehensive library for computational molecular biology
Pyfaidx
⭐
427
Efficient pythonic random access to fasta subsequences
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Seqan3
⭐
373
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
Bioinformatics One Liners
⭐
277
Bioinformatics one liners from Ming Tang
Pyfastx
⭐
211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Ntseq
⭐
204
JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis.
Soapdenovo2
⭐
197
Next generation sequencing reads de novo assembler.
Biosyntax
⭐
184
Syntax highlighting for computational biology
Gfatools
⭐
181
Tools for manipulating sequence graphs in the GFA and rGFA formats
Rasusa
⭐
156
Randomly subsample sequencing reads to a specified coverage
Genomics
⭐
154
A collection of scripts and notes related to genomics and bioinformatics
Pydna
⭐
140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
Redundans
⭐
121
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
Sibeliaz
⭐
113
A fast whole-genome aligner based on de Bruijn graphs
Swarm
⭐
110
A robust and fast clustering method for amplicon-based studies
Readfq
⭐
105
Fast multi-line FASTA/Q reader in several programming languages
Dna2vec
⭐
103
dna2vec: Consistent vector representations of variable-length k-mers
Isoquant
⭐
98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Seqfu2
⭐
96
🚀 seqfu - Sequece Fastx Utilities
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Bcalm
⭐
90
compacted de Bruijn graph construction in low memory
Cljam
⭐
87
A DNA Sequence Alignment/Map (SAM) library for Clojure
Wgd
⭐
74
Python package and CLI for whole-genome duplication related analyses
Aviary
⭐
62
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
Flexidot
⭐
56
Highly customizable, ambiguity-aware dotplots for visual sequence analyses
Fastv
⭐
56
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.
Transanno
⭐
54
accurate LiftOver tool for new genome assemblies
Dnaio
⭐
52
Efficiently read and write sequencing data from Python
Gccontent Benchmark
⭐
49
Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
Metacache
⭐
49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Macrel
⭐
48
Predict AMPs in (meta)genomes and peptides
Fastaq
⭐
45
Python3 scripts to manipulate FASTA and FASTQ files
Fluentdna
⭐
43
FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.
Assembly_improvement
⭐
39
Improve the quality of a denovo assembly by scaffolding and gap filling
Fuc
⭐
38
Frequently used commands in bioinformatics
Uniquekmer
⭐
33
Generate unique KMERs for every contig in a FASTA file
Bioawk Tutorial
⭐
30
Bioinf Commons
⭐
30
Bioinformatics library in Kotlin
Tidysq
⭐
28
tidy processing of biological sequences in R
Bac Genomics Scripts
⭐
28
Collection of scripts for bacterial genomics
Spacepharer
⭐
28
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
Vapid
⭐
27
VAPiD: Viral Annotation and Identification Pipeline
Biotoolbox
⭐
27
Tools for querying and analysis of genomic data
Helpful_commands
⭐
26
Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks.
Orfipy
⭐
25
Fast and flexible ORF finder
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.
Autopvs1
⭐
23
An automatic classification tool for PVS1 interpretation of null variants
Socru
⭐
23
Order and orientation of complete bacterial genomes
Fusiondirect.jl
⭐
23
(No maintenance) Detect gene fusion directly from raw fastq files
Smbl
⭐
22
SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.
Metacherchant
⭐
19
Bioinfo
⭐
19
Various bioinformatics tools
Wgs2ncbi
⭐
18
Toolkit for preparing genomes for submission to NCBI
Bionitio Python
⭐
18
Demonstrating best practices for bioinformatics command line tools
Fasql
⭐
18
DuckDB Extension for reading and writing FASTA and FASTQ Files
Mview
⭐
16
MView extracts and reformats the results of a sequence database search or multiple alignment.
Catsequences
⭐
15
A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses
Bioinformatics Tools
⭐
14
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
Mlst_check
⭐
14
Multilocus sequence typing by blast using the schemes from PubMLST
Scriptmanager
⭐
14
Rnalien
⭐
14
RNAlien - unsupervised RNA family model construction
Bionode Fasta
⭐
13
Streamable FASTA parser.
Lava
⭐
13
LAVA: Lightweight Assignment of Variant Alleles
Berokka
⭐
12
🍊 💫 Trim, circularise and orient long read bacterial genome assemblies
Smof
⭐
12
Explore and analyze biological sequence data
Fastaio.jl
⭐
11
Utilities to read/write FASTA format files in Julia
Bigbio
⭐
11
Big data bioinformatics repository
Psdm
⭐
10
Compute a pairwise SNP distance matrix from one or two alignment(s)
Protein Feature Extraction
⭐
10
Python code to extract features from Protein sequences for Machine Learning/Deep Learning
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).
Bioparser
⭐
9
C++ library for parsing several formats in bioinformatics
Pfasta
⭐
9
A Pedantic FASTA Parser and Tool Set
Seqshuffle.jl
⭐
9
Shuffle the string sequences such that the k-mer frequency is preserved in each string
Blss
⭐
8
A suite of unique bioinformatics tools for the brave explorer.
Hyraxabif
⭐
8
ABIF parser, writer and generator
Ipdmhc
⭐
8
Github for files currently published in the IPD-MHC FTP Directory hosted at the European Bioinformatics Institute
Db.rna16s
⭐
8
A comprehensive, compact, and automatically curated 16S database
Metacrast
⭐
8
MetaCRAST: reference-guided CRISPR detection in metagenomes
Pathogenie
⭐
7
Desktop tool for microbial genome annotation and gene detection
Kutils
⭐
7
A random collection of kotlin utilities
Python_scripts
⭐
7
scripts for parsing PDB, fasta, and GO
Bionim
⭐
7
A collection of useful algorithms and data structures for bioinformatics
Scanpav
⭐
7
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Popgen
⭐
7
Small scripts for population genetics analysis
Generic_genomics
⭐
7
small scripts, functions or bits of code for parsing genomic data
Circcode
⭐
7
A Python3-base pipeline for translated circular RNA(circRNA) identification
Biomisc
⭐
6
collection of miscellaneous command line bioinformatic scripts
Slim
⭐
6
A web app for environmental DNA metabarcoding analysis
Ebt
⭐
6
Evolutionary Bioinformatics Toolkit (EBT)
Covseq
⭐
6
CoV-Seq: COVID-19 Genomic Sequence Database and Visualization
Lava
⭐
6
LAVA: Longitudinal Analysis of Viral Alleles
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