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Search results for genome analysis
genome-analysis
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40 search results found
Hgvs
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226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Rasusa
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156
Randomly subsample sequencing reads to a specified coverage
Winnowmap
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131
Long read / genome alignment software
Intervene
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111
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
Earlgrey
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90
Earl Grey: A fully automated TE curation and annotation pipeline
Mccortex
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86
De novo genome assembly and multisample variant calling
Bacannot
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85
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
Dnabert_2
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72
The official implementation of DNABERT-2.
Helen
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52
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Teamteri
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50
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
Gala
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45
Long-reads Gap-free Chromosome-scale Assembler
Biocommons.seqrepo
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34
non-redundant, compressed, journalled, file-based storage for biological sequences
Cogclassifier
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27
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Blend
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26
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
Maxatac
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24
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Rawhash
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23
RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39
Score Assemblies
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20
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
Mspc
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18
Using combined evidence from replicates to evaluate ChIP-seq peaks
Codex
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17
A minimal genetic data explorer that processes all genetic information locally.
Bioutils
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16
provides common tools and lookup tables used primarily by the hgvs and uta packages
Ampliconreconstructorom
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14
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Ppspcp
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13
A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline
Nanorepeat
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13
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Codonu
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13
A python project for analysis of codon usage for gene or genome analysis
Gwastools
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13
Basic and fast GWAS functions for QQ and Manhattan plots (incl. gene names)
Genome On Diet
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11
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Genomicscourse
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11
For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics
Anyvar
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11
[in development] Proof-of-Concept variation translation, validation, and registration service
Positive Selection
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10
Scripts and procedures for detecting positively selected genes and codons in primates
Plasforest
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10
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
Metausat
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10
metaUSAT is a data-adaptive statistical approach for testing genetic associations of multiple traits from single/multiple studies using univariate GWAS summary statistics.
Hammlet
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10
Fast Bayesian Hidden Markov Model with Wavelet Compression
Genenotebook
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9
A collaborative notebook for genes and genomes
Everest
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9
Viral genome assemble and characterisation
Kec
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8
Unique sequence search by K-mer exclusion
Lescroart2023
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7
Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)
Ipat
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7
iPat allows you to perform GWAS and GS with drags and clicks!
Tutorials
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5
Tutorials for the crisprVerse
Plot Vcf
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5
visual analysis of your VCF files
Bio Bin
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5
Handy reusable bioinformatic scripts
1-40 of 40 search results
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