PPLine

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

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