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Single-cell DNA sequencing data analysis bioinformatics software tools

Single-cell genomics aims to provide new perspectives to our understanding of genetics by bringing the study of genomes to the cellular level. These tools are opening up new frontiers by dissecting the contributions of individual cells to the biology of ecosystems and…

scDNA-seq analysis steps

Most recent bioinformatics tools

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SIDR
Desktop

SIDR Simultaneous Isolation of genomic DNA and total RNA

Provides a method for the simultaneous isolation of genomic DNA and total RNA…

Provides a method for the simultaneous isolation of genomic DNA and total RNA from single cells. SIDR physically isolates total RNA, regardless of polyadenylation, from the single-cell lysate that…

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PaSD-qc
Desktop

PaSD-qc

Estimates quality and properties of single cell whole-genome sequencing (scWGS)…

Estimates quality and properties of single cell whole-genome sequencing (scWGS) data. PaSD-qc is an open source program that includes functionalities for detecting sub-chromosomal with amplification…

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LiRA
Algorithm

LiRA linked-Read analysis

Allows users to validate candidate somatic single nucleotide variation (sSNVs)…

Allows users to validate candidate somatic single nucleotide variation (sSNVs) occurring close to germline heterozygous SNPs (gHets). LiRA permits to determine false positive (FPs) sSNV calls from…

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SinCHet
Desktop

SinCHet SINgle Cell HETerogeneity

Can quantify cellular heterogeneity and identify novel candidate biomarkers.…

Can quantify cellular heterogeneity and identify novel candidate biomarkers. SinCHet is a MATLAB package with a graphical user interface (GUI) for visualization and user interaction, originally for…

Most popular analytical software and databases

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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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SPAdes
Desktop

SPAdes

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

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 from…

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