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Search results for c fasta

52 search results found

Seqtk ⭐ 1,148

Toolkit for processing sequences in FASTA/Q formats

BWK awk modified for biological data

Minigraph ⭐ 367

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

Pyfastx ⭐ 211

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

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Gfatools ⭐ 181

Tools for manipulating sequence graphs in the GFA and rGFA formats

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

Vcf Validator ⭐ 125

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

Fastx_toolkit ⭐ 109

FASTA/FASTQ pre-processing programs

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

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

Git repository for FASTA36 sequence comparison software

Scrappie ⭐ 81

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

Snp Dists ⭐ 68

Pairwise SNP distance matrix from a FASTA sequence alignment

Conterminator ⭐ 57

Detection of incorrectly labeled sequences across kingdoms

A genomics-proteomics toolkit

Gene prediction software

Utility program for extracting sequences from a fasta/fastq file

Blast2bam ⭐ 33

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

Uniquekmer ⭐ 33

Generate unique KMERs for every contig in a FASTA file

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

Mapcaller ⭐ 32

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

Spacepharer ⭐ 28

SpacePHARER CRISPR Spacer Phage-Host pAiRs 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.

Lr2rmats ⭐ 24

Long read to rMATS

Poseidon ⭐ 23

PoSeiDon: positive selection detection and recombination analysis pipeline

Tidehunter ⭐ 22

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Taxonomer_0.5 ⭐ 21

full taxonomer cython repository

Read alignment with a multi-genome reference

Tidehunter ⭐ 17

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

Methylcode ⭐ 16

Alignment and Tabulation of BiSulfite Treated Reads

Catsequences ⭐ 15

A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses

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

Ac Diamond ⭐ 14

AC-DIAMOND is a DNA-protein alignment tool

genomic alignment similarity search tool

Kontaminant ⭐ 14

Tool to look for contaminants, with a kmer database.

simple and not slow ORF caller

LAVA: Lightweight Assignment of Variant Alleles

Munge GenBank files into FASTA and tab-separated metadata

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

A Pedantic FASTA Parser and Tool Set

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

C Minhash ⭐ 9

Simple and fast MinHash implementation in C with Python wrapper

Library for Reading Bioinformatic Sequence Data in C

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

CAST v1.2.2, A C implementation of Compressively Accelerated Search Tools

Github for the TOPCONS2

Just a python fasta/q parser based on kseq.h

Parallel Smith-Waterman Alignment Software

Mica Aligner ⭐ 5

MICA-aligner is a new short-read aligner that is optimized in view of MIC's limitation and the extra parallelism inside each MIC core.

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