IDP-denovo

  • IDP-denovo is a tool for de novo transcriptome assembly and isoform annotation by hybrid sequencing.
  •  
  •     

Latest News: IDP-denovo_v.1 is released read more

Download and install IDP-denovo, read "readme" in code package for details.
   make
  
For impatient people
 
   ./idpdenovo  
   
e.g, ./idpdenovo scaffold=/user/shuhua/idpdenovo/test_data/scaffold.fa lr=/user/shuhua/idpdenovo/test_data/lr.fa leftSr=/user/shuhua/idpdenovo/test_data/leftSr.fa rightSr=/user/shuhua/idpdenovo/test_data/rightSr.fa For test (in directory "test_data"): "scaffold.fa", "lr.fa" "leftSr.fa" "rightSr.fa"

Step 1 - SR-scaffold extension and k-mer cluster

        scaffoldExtend   
         
scaffold.fa is from Oases output (transcripts.fa), In "LR.fa", tags of sequences format are "lr1,lr2..."
       kCluster   
        
To cluster unaligned LRs with k-mer clustering method Output includes a TXT file and a Log file

Step 2 - Isoform annotation

 kCluster  kmer_size > clusterOutput 2> clusterLog
         
To cluster unaligned LRs with k-mer clustering method, output a TXT file and a log file to track progress of clustering

Step 3 - Quantification

 MLE   python_path code_path SR_length  
Output file is "refSeq_MLE_output1.tab" to tell SR coverage for each transcript. IDP-denovo will outupt LR coverage. SR align to pseudo-reference with HISAT LR align to transcripts with GMAP