Phy-Mer: Mitochondrial haplogroup classifier @ MSeqDR             

Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier.
It supports input in fasta (single or multiple), single sample fastq, bam, csv formats

Option 1: Copy and Paste Your Input Below

Input format: fasta fastq csv hgvs/vcf/classic (For VCF, must use the first 5 columns only)
  Email   notice me when finished

Option 2: Upload Input File

Drag & Drop fasta, fastq, bam, or csv file here...

Files available:
   
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 Help file sample input: fasta fastq bam csv

Phy-Mer Settings:

 SYNOPSIS
 ./Phy-Mer.py [--verbose] [--print-ranking] [--def-snps=haplogroup_def_motifs.csv] [--min-DoC=10] Library.txt INPUT_1 [INPUT_2 ... INPUT_X]

 Mandatory arguments:

   Library.txt: Provided with the package: PhyloTree_b16_k12.txt

   INPUT_X: One or more input files from the text box, or file list above. Supports FASTA, FASTQ, or BAM format, or variant list in csv format. BAM must be aligned bam file where Phy-Mer uses only reads in the "MT" "chromosome" (['M','MT','chrM','chrMT','chrMt','Mt','ChrM','ChrMT','ChrMt','CHRM','CHRMT','CHRMt']) discarding all the rest of the data.

   Input format: Please limit to mitochondrial sequences, and file size under 50 MB.

 Optional arguments:

  --verbose: Print step by step process.

  --print-ranking: Print top 5 results instead of the best match.

  --def-snps: Show haplogroup defining snps from in Build_16_-_rCRS-based_haplogroup_motifs.csv to top matches.

  --min-DoC: Minimal number of occurrences of a K-mer to be considered, only apply to BAM inputs.

Citation:

Daniel Navarro-Gomez, Jeremy Leipzig, Lishuang Shen, Marie Lott, Alphons P.M. Stassen, Douglas C. Wallace, Janey L. Wiggs, Marni J. Falk, Mannis van Oven, and Xiaowu Gai
Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier. Bioinformatics 2014: btu825v1-btu825.