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High-throughput sequencing software tools

 

Whole-genome sequencing

1463 tools

   
 

Whole-exome sequencing

129 tools

   
 

De novo genome sequencing

180 tools

   
 

RNA-seq

588 tools

   
 

ChIP-seq

252 tools

   
 

Small RNA-seq

103 tools

   
 

BS-seq

181 tools

   
 

Metagenomic sequencing

359 tools

   
 

MeRIP-seq

4 tools

   
 

RIP-seq/CLIP-seq

29 tools

   
 

3C/4C/5C/Hi-C/ChIA-PET

60 tools

   
 

Amplicon sequencing

8 tools

   
 

GBS

7 tools

   
 

Pool-seq

75 tools

   
 

RAD-seq

11 tools

   
 

Rep-seq

32 tools

   
 

Strand-seq

1 tools

   
 

Deep mutational scanning

2 tools

   
 

GRO-seq

4 tools

   
 

Tn-seq

9 tools

   
 

CAGE

9 tools

   
 

Single-cell RNA-seq

45 tools

   
 

DGE

4 tools

   
 

dRNA-seq

4 tools

   
 

RNA structurome

10 tools

   
 

de novo ChIP-seq

1 tools

   
 

DNase-seq

14 tools

   
 

MNase-seq

8 tools

   
 

Ribo-seq

6 tools

   
 

ChIP-exo

3 tools

   
 

HT-SELEX

7 tools

   
 

PARE

8 tools

   
 

MeDIP-seq

11 tools

   
 

MethylCap-seq

5 tools

   
 

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oxBS/TAB/fCAB/CAB-seq

5 tools

   
 

Metatranscriptomics

9 tools

 
 

CRISPR-Cas9 knockout screening

4 tools