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Search results for c plus plus fasta
c-plus-plus
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fasta
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88 search results found
Vsearch
⭐
605
Versatile open-source tool for microbiome analysis
Seqan
⭐
444
SeqAn's official repository.
Seqan3
⭐
373
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
Gffread
⭐
288
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
Racon
⭐
195
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:
Aligngraph
⭐
165
Algorithm for secondary de novo genome assembly guided by closely related references
Racon
⭐
127
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
Branch
⭐
122
Boosting RNA-Seq assemblies with partial or related genomic sequences
Sibeliaz
⭐
113
A fast whole-genome aligner based on de Bruijn graphs
Swarm
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110
A robust and fast clustering method for amplicon-based studies
Skesa
⭐
99
SKESA assembler
Assembly Stats
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92
Get assembly statistics from FASTA and FASTQ files
Idba
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80
Biobambam2
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79
Tools for early stage alignment file processing
Biobloom
⭐
70
Create Bloom filters for a given reference and then use it to categorize sequences
Pizzly
⭐
67
Fast fusion detection using kallisto
Cas Offinder
⭐
63
An ultrafast and versatile algorithm that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases.
Genmap
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62
GenMap - Fast and Exact Computation of Genome Mappability
Dbg2olc
⭐
60
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.
Flexbar
⭐
59
flexible barcode and adapter removal
Cobs
⭐
58
COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
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.
Fastahack
⭐
54
utilities for indexing and sequence extraction from FASTA files
Cryfa
⭐
51
A secure encryption tool for genomic data
Rufus
⭐
49
RUFUS k-mer based genomic variant detection
Metacache
⭐
49
memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping
Svmu
⭐
42
A program to call variants from genome alignment
Reindeer
⭐
42
REINDEER REad Index for abuNDancE quERy
Pbsim2
⭐
40
PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores
Consent
⭐
40
Scalable long read self-correction and assembly polishing with multiple sequence alignment
Fqfeeder
⭐
40
Self-contained, multi-threaded fasta/q parser
Antonie
⭐
36
Antonie is an integrated, robust, reliable and fast processor of DNA reads
Kseqpp
⭐
34
Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)
Bamhash
⭐
32
Rapsearch2
⭐
31
Reduced Alphabet based Protein similarity Search
Tidysq
⭐
28
tidy processing of biological sequences in R
Fuseq
⭐
27
Fxtools
⭐
25
FxTools: a comprehensive toolkit for FASTA and FASTQ file manipulation
Piledriver
⭐
24
Basic, no assumptions, multi-pileup
Ust
⭐
20
Wasm32 Wasi Benchmark
⭐
19
Fastafs
⭐
19
toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files
Gimbricate
⭐
18
recompute GFA link overlaps
Fasql
⭐
18
DuckDB Extension for reading and writing FASTA and FASTQ Files
Nanovar Archived
⭐
17
Archived version 1.0.2
Daccord
⭐
17
d'accord is a non hybrid long read consensus program based on local de Bruijn graph assembly
Cammiq
⭐
16
Metagenomics microbial abundance quantification
Ogap
⭐
16
gap opening realigner for BAM data streams
Rabbitmash
⭐
16
RabbitMash: an efficient highly optimized implementation of Mash.
Salmontools
⭐
16
Useful tools for working with Salmon output
Dynamicdbg
⭐
16
Practical Dynamic de Bruijn Graphs
Karp
⭐
16
Accurate and fast taxonomic classification using pseudoaligning
Commet
⭐
13
Comparing and combining multiple metagenomic datasets
Apollo
⭐
12
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-techn
Gakco Svm
⭐
12
ECML16: GaKCo: a Fast Gapped k-mer string Kernel using Counting
Bwise
⭐
11
de Bruijn Workflow using Integral information of Short pair End reads
Lightstringgraph
⭐
10
Lightweight String Graph Construction
Vbt Trioanalysis
⭐
10
Bioparser
⭐
9
C++ library for parsing several formats in bioinformatics
Chopstitch
⭐
9
Finding putative exons and constructing splicegraphs using Trans-ABySS contigs
Mmseqs
⭐
9
Bioio
⭐
9
Lightweight C++ library for reading FASTA and FASTQ files.
Genetics
⭐
8
A boost library for genetic searches
Ribomap
⭐
8
Npge
⭐
8
Nucleotide PanGenome explorer
Biocpp Io
⭐
8
BioC++ Input/Output library
Lime
⭐
7
Fastx_read_count
⭐
7
Tiny program to count reads in FASTA/FASTQ files
Carnac Lr
⭐
7
Cdbfasta
⭐
7
Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files
Lrcstats
⭐
7
An open-source pipeline for benchmarking DNA long read correction algorithms for third generation sequencing technology
Sdm
⭐
6
Fast tool for sequence related tasks
Tgt_package
⭐
6
Generate A3M and TGT file from a given sequence in FASTA format.
Multi Genome Reference
⭐
6
A program to generate a graph which presents a simplified representation of several full length genomes
Aselux
⭐
6
Pufferfish
⭐
5
Super simple, super lightweight dna compression tool
Fxtract
⭐
5
Extract sequences from a fastx file given a subsequence or identifier
Mlehaplo
⭐
5
Maximum Likelihood Estimation for Viral Populations
Vcf2fas
⭐
5
fasta files from vcf file(s)
Pdb2fasta
⭐
5
change format from pdb to fasta .python file change from https://gist.github.com/jameslyons/00cad4f1ab6a49c .And C++ file is written by myself.
Slope Spam
⭐
5
Svaha
⭐
5
Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
Dynboss
⭐
5
DynamicBOSS
Quaff
⭐
5
FASTA/FASTQ alignment
Mrgbp
⭐
5
Metagenomic Binning through Multi-resolution Genomic Binary Patterns
Jellyfish
⭐
5
Fork of the jellyfish kmer counter. Here is the description copied from their site: JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting th
Sigclust
⭐
5
k-means clustering for biological sequences using topological signatures
Pastis
⭐
5
Distributed Protein Sequence Aligner
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