Aquila_Umap

conda install aquila_umap

(Please ensure channels are properly setup for bioconda before installing)

Usage

aquila_umap --fa_folder /path/to/fasta/ --fa_name sample.fa  --out_dir /path/to/result/ --chr_start 1 --chr_end 1 --chr_thread 4

*Required parameters

–fa_folder: the directory which you save the reference fa files.

–fa_name: the name of the reference fa file.

–out_dir: the directory to save the output results.

*Optional parameters

–kmer_len , default = 100, the length of generated kmers.

–mapq_thres: default = 50000 (50kb), the MAPQ threshold to keep unique mapping kmers.

—chr_thread , default = 2, number of threads for processing chromosome,

–chr_start, –chr_end: if you only process some chromosomes or only one chromosome. For example: use “–chr_start 1 –chr_end 5” will process chromsomes 1,2,3,4,5. Use “–chr_start 2 –chr_end 2” will only assemlby chromosome 2.

A practical example

Download Rhesus macaque (Macaca mulatta, ftp://ftp.ensembl.org/pub/release-97/fasta/macaca_mulatta/dna/ ) genome fasta file from HERE.

Your folder structure should be as follows :

Rhesus_macaque
    |-fasta
        |-macaca_mulatta.fa

“macaca_mulatta.fa” is the fasta file you have just downloaded.

Then edit the second block and run the whole notebook.

fa_folder = "path/to/Rhesus_macaque/fasta/"
fa_name = "macaca_mulatta.fa"
out_dir = "path/to/Rhesus_macaque/output/"
start = 1
end = 21      # 21 correponds to "chrX" for rhesus macaque 
kmer_len = 100 
mapq_thres = 20
bowtie_thread = 20 

When finished, you will get:

Rhesus_macaque
|-fasta
|   |-macaca_mulatta.fa
|
|-output
    |-Uniqness_map
        |-uniq_map_chrxxx.p
        |-uniq_map_chrxxx.p
        |-uniq_map_chrxxx.p
        ...

The final results are stored in Uniqness_map folder.