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PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data.
PPLine provides:
- read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery
- gene and transcript expression estimation (HTSeq-count/Cufflinks)
- SNP calling with BQSR and indel realignment (samtools/GATK)
- variant annotation (Annovar)
- novel transcripts discovery (Cufflinks)
- predicting proteotypic peptides and creating ref/alt proteins fasta-database
- integration of the results
Features
- SNP calling
- SNP annotation
- Gene expression quiantification
- Transcript expression quantification
- Predicting proteotypic peptides
- Novel transcripts discovery
- Workflow automation
Categories
Bio-InformaticsFollow PPLine
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