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707 search results found

Pybsaseq ⭐ 27

A novel algorithm with high detection power for BSA-Seq data analysis - the significant structural variant method

VAPiD: Viral Annotation and Identification Pipeline

Is_mapper ⭐ 26

IS mapping software

Genome-wide imputation pipeline

Metacompass ⭐ 26

MetaCompass: Reference-guided Assembly of Metagenomes

Pytorch Cns ⭐ 26

Generalized Compressed Network Search with PyTorch

Clusterdbanalysis ⭐ 26

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

Dbnet_tensorflow ⭐ 26

Speciesprimer ⭐ 26

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

Teloclip ⭐ 26

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

paprica - PAthway PRediction by phylogenetIC plAcement

Spraynpray ⭐ 25

Rapid and simple taxonomic profiling of genome and metagenome contigs

Pathoscope ⭐ 25

Pathoscope: Species identification and strain attribution with unassembled sequencing data

Neat Python ⭐ 25

Genetic learning algorithm implementation for simulations, games, or general machine learning problems

2018 Ncbi Lineages ⭐ 25

Extract lineage CSVs from NCBI for use with sourmash lca.

TELR is a fast non-reference transposable element detector from long read sequencing data.

Pore C Snakemake ⭐ 25

Vcf2fasta ⭐ 25

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

Annogesic ⭐ 25

ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes

Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data

Te_density ⭐ 24

Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/article

INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomic surveillance

miRge - microRNA alignment software for small RNA-seq data, now at v2.0

Metasanity ⭐ 24

Pipeline for major biological analyses.

Public_scripts ⭐ 24

collection of bioinformatic scripts

Tandem repeat expansion detection or genotyping from long-read alignments

Bioinformatics Course 2020 ⭐ 23

Find_circ ⭐ 23

tools to find circRNAs in RNA-seq data

Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

1000 Genomes Genetic Maps ⭐ 23

Genetic maps interpolated to sites in the 1000 Genomes project

Microbecensus ⭐ 23

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

Site Identification from Short Read Sequences.

Python library and scripts for retrieval and storage of genomics data in HDF5 format

Order and orientation of complete bacterial genomes

Sigprofilersinglesample ⭐ 22

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.

Iggsearch ⭐ 22

Metagenomic species profiling with enhanced coverage of the human gut microbiome

Repenrich2 ⭐ 22

RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.

GC Skew Test for Bacterial Genomes

Standard database for the TBProfiler tool

Pipeline Pinfish Analysis ⭐ 22

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Binning_refiner ⭐ 22

Improving genome bins through the combination of different binning programs

GRAph-based Finding of Individual Motif Occurrences

A python implementation of flux balance analysis to model microbial metabolism

Pipeline Umi Amplicon ⭐ 21

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

Biohansel ⭐ 21

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes

Metalign ⭐ 21

Metalign: efficient alignment-based metagenomic profiling via containment min hash

Repenrich ⭐ 21

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

Swiftortho ⭐ 21

A high performance tool to identify orthologs and paralogs across genomes.

Nanolyse ⭐ 21

Remove lambda phage reads from a fastq file

Finding prophage regions in bacterial genomes using brute force

Coessentiality ⭐ 21

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)

Jbrowse Jupyter ⭐ 21

A python package for showing JBrowse views

mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads

Tool to estimate genome quality of microbial eukaryotes

Genome Server 21 ⭐ 20

Serve your genotypes and phenotypes via an API for satoshis

Primer Schemes ⭐ 20

Primer schemes for real-time genome epidemiology

Porthomcl ⭐ 20

Parallel implementation of OrthoMCL

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Snpedia 23andme ⭐ 20

Analyse a genome file from 23andMe using the data on snpedia.com

Primerdesign ⭐ 20

A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

Checkvcf ⭐ 20

Sanity check Variant Call Format (VCF) files.

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.

Contiguator ⭐ 20

Bacterial genomes finishing tool for structural insights on draft genomes

Score Assemblies ⭐ 20

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

Guessmylt ⭐ 20

An efficient way to guess the library type of your RNA-Seq data.

Liftoverplink ⭐ 20

A wrapper for liftOver for converting plink genotype data between different genome reference builds

A toolkit for prokaryotic comparative genomics

whole genome MLST analysis

A set of tools for modelling ancestry patterns along the genome.

Slideseq Tools ⭐ 20

Tools for analyzing Slide-seq data

Full_stack_chromhmm_annotations ⭐ 20

Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes

Metagenomic binning based on Hi-C data

Evolution simulator with extinct lineages

A message queue for genomic surveillance

Mashing Pumpkins ⭐ 19

Minhash and maxhash library in Python, combining flexibility, expressivity, and performance.

Sistr_cmd ⭐ 19

SISTR (Salmonella In Silico Typing Resource) command-line tool

Architect ⭐ 19

Scaffolding genomes using synthetic long read clouds

Bioinformatics Technology Lab common code library

Pynnotator ⭐ 19

This is a Genome Annotation Framework developed with the goal of annotating VCF files (Exomes or Genomes) from patients with Mendelian Disorders.

Epicov_downloader ⭐ 19

Download all EpiCoV sequcnes from GISAID

Homblocks ⭐ 19

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

Helmsman ⭐ 19

highly-efficient & lightweight mutation signature matrix aggregation

Approach to identify simple and complex structural genomic rearrangements using a randomized approach

Danbing Tk ⭐ 18

Toolkit for VNTR genotyping and repeat-pan genome graph construction

Seqsero2 ⭐ 18

Annotated Genome Optimization Using Transcriptome Information

Reconcnv ⭐ 18

visualize CNV data from targeted capture based sequencing data

Compare Annotations ⭐ 18

A script for comparing old vs new versions of genome annotations

Genomic Association Tester

For original Nature Biotechnology Publication (Q1 2012)

Samchain ⭐ 18

G2gtools ⭐ 18

Personal diploid genome creation and coordinate conversion

Sigprofilersimulator ⭐ 18

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Seqqscorer ⭐ 18

Mof Search ⭐ 18

BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours

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