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
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Drag & Drop fasta, fastq, bam, or csv file here...
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Files available:
**To keep your data private from public users, please register and login  sample input: fasta fastq bam csv |
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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. |
