PPLine
SNP calling, annotation and gene/transcripts expression quantification
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...