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Table 1 Comparison of available tools with functionalities possibly overlapping with ALFA. This table shows that none of them offers all capabilities provided by ALFA

From: ALFA: annotation landscape for aligned reads

 

BEDOPS [11]

BEDTools [10]

featureCounts [25]

CAP-miRSeq [8]

HOMER [9]

RSeqQC [26]

bam2x [12]

CEAS [7]

ALFA

One line call

   

✔⃞

✔⃞

✔⃞

✔⃞

✔⃞

✔⃞

Multiple samples

  

✔⃞

✔⃞

    

✔⃞

Nucleotide resolution

✔⃞

✔⃞

      

✔⃞

Hierarchical priorities

  

✔⃞

 

✔⃞

✔⃞

✔⃞

✔⃞

✔⃞

Enrichment score

     

✔⃞

 

✔⃞

✔⃞

Categories

✔⃞

✔⃞

✔⃞

 

✔⃞

✔⃞

✔⃞

✔⃞

✔⃞

Biotypes

✔⃞

✔⃞

✔⃞

✔⃞

    

✔⃞

Graphical output

   

✔⃞

  

✔⃞

✔⃞

✔⃞

Any NGS data

✔⃞

✔⃞

✔⃞

  

✔⃞

✔⃞

 

✔⃞