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Single-cell assemblers

Whole genome amplification by the multiple displacement amplification (MDA) method allows sequencing of genomes from single cells of bacteria that cannot be cultured. However, genome assembly is challenging because of highly non-uniform read…
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SPAdes
Desktop

SPAdes

A single-cell assembler for capturing and sequencing “microbial dark…

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes…

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Velvet-SC
Desktop

Velvet-SC Velvet Single Cell

An approach tailored package for single cell Illumina sequences that…

An approach tailored package for single cell Illumina sequences that incorporates a progressively increasing coverage cutoff. Velvet-SC allows variable coverage datasets to be utilized effectively…

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SCG
Desktop

SCG Single Cell Genotyper

An interpretable probabilistic model, simultaneously addressing technical…

An interpretable probabilistic model, simultaneously addressing technical sources of noise in single-cell sequencing data and inferring a discrete set of genotypes present in a cell population and…

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Monovar
Desktop

Monovar

A statistical method for detecting and genotyping single-nucleotide variants in…

A statistical method for detecting and genotyping single-nucleotide variants in single-cell data. Monovar exhibited superior performance over standard algorithms on benchmarks and in identifying…

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Ginkgo
Desktop
Web

Ginkgo

Allows automated and interactive analysis of single-cell copy-number…

Allows automated and interactive analysis of single-cell copy-number variations. Ginkgo enables quality assessment, GC bias correction, segmentation, copy-number calling, visualization and…

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IDBA-UD
Desktop

IDBA-UD

A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data…

A iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

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SCITE
Desktop

SCITE

A stochastic search algorithm to identify the evolutionary history of a tumor…

A stochastic search algorithm to identify the evolutionary history of a tumor from noisy and incomplete mutation profiles of single cells. SCITE comprises a flexible Markov chain Monte Carlo sampling…

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OncoNEM
Desktop

OncoNEM Oncogenetic Nested Effects Model

A probabilistic method for inferring intra-tumor evolutionary lineage trees…

A probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. The OncoNEM algorithm consists of two main parts: (1) a…

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Squeezambler
Desktop

Squeezambler

A method to sequence and de novo assemble all distinct genomes present in a…

A method to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather…

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Canu
Desktop

Canu

Is specifically designed for noisy single-molecule sequences. Canu introduces…

Is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while…

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MeCorS
Desktop

MeCorS

Corrects chimeric reads and sequencing errors in Illumina data generated from…

Corrects chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). MeCorS uses sequence information derived from accompanying metagenome sequencing to…

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SiFit
Desktop

SiFit

Reconstructs phylogenetic tree from noisy mutation profile of single cells.…

Reconstructs phylogenetic tree from noisy mutation profile of single cells. SiFit employs a heuristic search algorithm to infer the Maximum Likelihood (ML) phylogenetic tree under a finite-site model…

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HyDA
Desktop

HyDA Hybrid De novo Assembler

Demonstrates the power of coassembly of multiple single-cell genomic data sets…

Demonstrates the power of coassembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics.…

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SmashCell
Desktop

SmashCell Simple Metagenomics Analysis SHell-for sequences from single Cells

Automates the main steps in microbial genome analysis-assembly, gene…

Automates the main steps in microbial genome analysis-assembly, gene prediction, functional annotation-in a way that allows parameter and algorithm exploration at each step in the process. It also…

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SCICAST
Desktop

SCICAST Single Cell Iterative Clustering and Significance Testing

Automates many of the repetitive steps of analyzing single cell sequencing…

Automates many of the repetitive steps of analyzing single cell sequencing data. SCICAST could be used for (i) clustering and subclustering of data to identify ‘stable’ sets of cells, (ii)…

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