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Search results for c genomics
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genomics
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48 search results found
Minimap2
⭐
1,613
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Bwa
⭐
1,282
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Minigraph
⭐
367
Proof-of-concept seq-to-graph mapper and graph generator
Genometools
⭐
261
GenomeTools genome analysis system.
Bedops
⭐
244
🔬 BEDOPS: high-performance genomic feature operations
Wgsim
⭐
188
Reads simulator
Gfatools
⭐
181
Tools for manipulating sequence graphs in the GFA and rGFA formats
Biowasm
⭐
165
WebAssembly modules for genomics
Bio Playground
⭐
146
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
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
Cgranges
⭐
144
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
Psmc
⭐
120
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Gkl
⭐
98
Accelerated kernel library for genomics
Mccortex
⭐
86
De novo genome assembly and multisample variant calling
Bgt
⭐
76
Flexible genotype query among 30,000+ samples whole-genome
Hickit
⭐
69
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
Fermi
⭐
68
A WGS de novo assembler based on the FMD-index for large genomes
Fermi Lite
⭐
67
Standalone C library for assembling Illumina short reads in small regions
Dna Nn
⭐
51
Model and predict short DNA sequence features with neural networks
Unimap
⭐
49
A fork of minimap2 optimized for assembly-to-reference alignment
Bio Pipeline
⭐
45
My collection of light bioinformatics analysis pipelines for specific tasks
Sample
⭐
44
Performs memory-efficient reservoir sampling on very large input files delimited by newlines
Lrsim
⭐
38
10x Genomics Reads Simulator
Variantkey
⭐
34
Numerical Encoding for Human Genetic Variants
Plastid
⭐
32
Position-wise analysis of sequencing and genomics data
Genomicsbench
⭐
27
A benchmark suite to study the performance characteristics of genomics applications
Flagger
⭐
26
Evaluating genome assemblies
Pybbi
⭐
24
Python bindings to UCSC BigWig and BigBed library
Scaff10x
⭐
20
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
Gdsfmt
⭐
18
R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)
Hapo G
⭐
18
Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
Metarna
⭐
17
Find target sites for the miRNAs in genomic sequences
Chromeister
⭐
16
A dotplot generator for large chromosomes
Mapping Iterative Assembler
⭐
15
Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria
Hash10x
⭐
14
a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly
Secphase
⭐
12
Phasing reads with secondary alignments
Stormbitmaps
⭐
11
Fast algorithms for computing XX^T for binary matrices
Bedmatrix
⭐
10
A matrix-like wrapper around PLINK .bed files
Scanpav
⭐
7
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Nanoplexer
⭐
6
Tool for demultiplexing Nanopore barcode sequence data
Kalis
⭐
6
kalis: High Performance Li & Stephens Local Ancestry Inference
Tersect
⭐
6
Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.
Genarchbench
⭐
5
Genomics benchmark suite targeting the Arm architecture. Public/mirror repository of GenArchBench (https://gitlab.bsc.es/Lorien/genarchbench).
Tatajuba
⭐
5
Identification and classification of homopolymeric tracts from reads.
Variantkey Nim
⭐
5
nim-wrapper for variantkey -- (chrom, pos, ref, alt) -> uint64
Seqcode
⭐
5
Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data
Conga
⭐
5
CONGA: COpy Number Genotyping in Ancient genomes and low-coverage sequencing data
Pareben
⭐
5
Parallel Implementations of the Empirical Bayesian Elastic Net Cross-Validation in R
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1-48 of 48 search results
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