960 Open source projects that are alternatives of or similar to tiptoft

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

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Multilocus sequence typing by blast using the schemes from PubMLST

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Finds SNP sites from a multi-FASTA alignment file

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A fast tool for hybrid genome assembly of long and short reads

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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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Real-time species-typing visualisation for nanopore data.

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🔬 BEDOPS: high-performance genomic feature operations

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Fast alignment and preprocessing of chromatin profiles

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cython + htslib == fast VCF and BCF processing

An ultrafast memory-efficient short read aligner

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Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Ultrafast sequence typing and gene detection from NGS raw reads

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Long read / genome alignment software

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Close assembly gaps using long-reads at high accuracy.

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Reference-based transcript discovery from long RNA read

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Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

A faster lmm for GWAS. Supports GPU backend.

Toolkit for preparing genomes for submission to NCBI

Provide R access to the NCI Genomic Data Commons portal.

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Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

A simple command-line tool to download data from Joint Genome Institute databases

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

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Ploidy agnostic phasing pipeline and algorithm

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An open-access bioinformatics text

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion