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Search results for c genome
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genome
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114 search results found
Star
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1,647
RNA-seq aligner
Bedtools2
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876
bedtools - the swiss army knife for genome arithmetic
Genometools
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261
GenomeTools genome analysis system.
Pyfastx
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211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Giggle
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207
Interval data structure
Kent
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197
UCSC Genome Browser source tree. Stable branch: "beta".
Soapdenovo2
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197
Next generation sequencing reads de novo assembler.
Genrich
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158
Detecting sites of genomic enrichment
Lancet
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145
Microassembly based somatic variant caller for NGS data
Winnowmap
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131
Long read / genome alignment software
Pufferfish
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104
An efficient index for the colored, compacted, de Bruijn graph
Minimap
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101
This repo is DEPRECATED. Please use minimap2, the successor of minimap.
Mccortex
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86
De novo genome assembly and multisample variant calling
Genefuse
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86
Gene fusion detection and visualization
Penncnv
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84
Copy number vaiation detection from SNP arrays
Hera
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74
Mocha
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70
MOsaic CHromosomal Alterations (MoChA) caller
Fermi
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68
A WGS de novo assembler based on the FMD-index for large genomes
Crisporwebsite
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64
All source code of the crispor.org website
Genomealignmenttools
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49
Tools for improving the sensitivity and specificity of genome alignments
Pauvre
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43
Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
Snap
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41
Gene prediction software
Lrsim
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38
10x Genomics Reads Simulator
Pblat
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37
parallelized blat with multi-threads support
Bloomfiltertrie
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36
An alignment-free, reference-free and incremental data structure for colored de Bruijn graph with application to pan-genome indexing.
Andi
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34
♥ Efficient Estimation of Evolutionary Distances
Desalt
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34
deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
Uniquekmer
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33
Generate unique KMERs for every contig in a FASTA file
Mapcaller
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32
MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
Wtdbg
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30
A fuzzy Bruijn graph approach to long noisy reads assembly
Sff2fastq
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30
extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
Debga
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28
de Bruijn Graph-based read aligner
Spacepharer
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28
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
Gem3 Mapper
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27
GEM-Mapper v3
Genasm
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26
Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis" at https://people.inf.ethz.ch/omutlu/pub/GenASM-appro
Flagger
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26
Evaluating genome assemblies
Vgp Tools
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26
Igenomics
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26
The first app for Mobile DNA Sequence Alignment and Analysis
Blink
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25
BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions
Fqgrep
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25
An approximate sequence pattern matcher for FASTQ/FASTA files.
Cesar2.0
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25
Aegean
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23
Integrated toolkit for analysis and evaluation of annotated genomes
Promotech
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21
Machine-learning-based general bacterial promoter prediction tool.
Gmap Gsnap
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21
*UNOFFICIAL, UNMAINTAINED and OUTDATED*: This was an unofficial archive of GMAP-GSNAP releases. Please use the original website for current versions of the source code.
Kart
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21
Kart: A divide-and-conquer algorithm for NGS read mapping with high error tolerance
Clamms
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20
CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
Mrsfast
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20
mrsFAST: micro-read substitution-only Fast Alignment Search Tool
Bwbble
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20
Read alignment with a multi-genome reference
Scaff10x
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20
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Tardis
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20
Toolkit for automated and rapid discovery of structural variants
Crispr Analyser
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19
C++ package for analysing CRISPR off targets
Mashing Pumpkins
⭐
19
Minhash and maxhash library in Python, combining flexibility, expressivity, and performance.
Gengen
⭐
19
A set of software tools to facilitate GWAS analysis
Bri
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18
Bam Read Index - Extract alignments from a bam file by readname
Hapo G
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18
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
Tailseeker
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18
Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
Linkedsv
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18
G Phocs
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18
G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.
Wise3
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17
The 3rd incarnation of the Wise package for sequence analysis
Flash2
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17
Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
Virulign
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17
VIRULIGN: fast codon-correct alignment and annotation of viral genomes
Etching
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16
Ultra-fast, high-performing structural variation (SV) detector
Bwa Aln Xeon Phi 0.5.10
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16
bwa-aln-xeon-phi optimizes bwa aln performance on both Xeon and Xeon Phi platform, and support symmetric running model on Xeon and Xeon Phi hybrid nodes.
Alignstats
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16
Comprehensive alignment, whole-genome coverage, and capture coverage statistics.
Bitmapperbs
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16
BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Chromeister
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16
A dotplot generator for large chromosomes
Eagle
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15
Airlift
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15
AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)
Valor
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14
variation discovery using long range information in linked-reads
Hash10x
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14
a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly
Hupan
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14
Human pan-genome analysis pipeline
Lava
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13
LAVA: Lightweight Assignment of Variant Alleles
Crisflash
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13
Mmp
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12
MEM mapper prototype
Bcfanno
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12
A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file
Igd
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12
A high-performance search engine for large-scale genomic interval datasets
Solidbin
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11
A genome binning method for contig binning, based on semi-supervised spectral clustering method.
Panito
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11
Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
Topmed_freeze3_calling
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10
TOPMed Freeze 3 variant calling pipeline
Genome Privacy
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10
Protocols for Secure Genomic Computation
Mpd C
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10
Multiplex Primer Design
Dnarm
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10
DNA read mapper will map short reads to the entire genome using all of your cores -- and GPU too
Psmcr
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9
R Port of psmc
Gsalign
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9
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
Genome Indexing On Gpu
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9
The project involves parallelizing the construction of suffix arrays on the GPU for the purpose of genome indexing.
Debwt
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9
A efficient method to construct BWT index of a given DNA sequence, especially useful for gigantic and high similar genome.
Lasv
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9
laSV is a software package that employs local assembly to detect structural variations from whole-genome high-throughput sequencing datasets
Grabb
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9
GRAbB (Genome Region Assembly by Baiting) is a program designed to assemble selected regions of the genome or transcriptome using reference sequences and NGS data.
Quick Mer2
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8
Demographicinference
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8
Scripts to compare models of divergence using diffusion approximation (dadi)
Divtime
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8
Bayesian molecular clock dating tutorial with genome-scale datasets
Dot2dot
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7
Dot2dot: Accurate Whole-Genome Tandem Repeats Discovery
Scanpav
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7
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Pecaller
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7
map and call next generation genomic sequencing
Darrc
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7
DARRC is a new alignment-free and reference-free compression method that addresses the problem of pan-genome compression by encoding the sequences of a pan-genome as a guided de Bruijn Graph. The novelty of this method is its ability to incrementally update DARRC archives with new genome sequences without full decompression of the archive. DARRC can compress both single-end and paired-end read sequences of any length using all symbols of the IUPAC nucleotide code.
Scaffhic
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7
Pipeline for genome scaffolding by modelling distributions of HiC pairs
Hpg Methyl
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7
An ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapper and methylation extractor.
Mrcanavar
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7
micro-read Copy Number Variant Regions finder
Sideretro
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7
A pipeline for detecting Somatic Insertion of DE novo RETROcopies
Shrimp
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6
SHRiMP is a software package for aligning genomic reads against a target genome.
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