linux-64 yukaiquan 1962568272@qq.com
Required software tools (third party, please install them according to instructions provided at respective links; e.g. by a conda environment):
conda install -c bioconda samtools
conda install -c conda-forge pandas
conda install -c bioconda pybedtoolspython misa_multiprocessing.py -h
usage: python misa_multiprocessing.py [-h] [--version] -g GENOME [-c CHR] [-t THREADS]
whole genome ssr find and primer design. Author:yukaiquan; Email:1962568272@qq.com
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
-g GENOME, --genome GENOME
Fatsa genome, should include all sequences from genome file.
-c CHR, --chr CHR Chromosome name, should be in the format of chr1A,chr2A,chr3A...(default is all chromosomes).
-t THREADS, --threads THREADS
The number of threads (default is 1).
Example:
python kq_misa.py -g SFS.fasta -t 1\ls
Avena_eriantha.fasta.gz Avena_eriantha.fasta.gz.fai Avena_eriantha.fasta.gz.gzi misa.ini misa_multiprocessing.py misa.plI have a genome file with 7 chromosomes.
cat Avena_eriantha.fasta.gz.fai
AE1 588203704 5 60 61
AE2 555382095 598007110 60 61
AE3 551069265 1162645579 60 61
AE4 534821622 1722899337 60 61
AE5 529955746 2266634658 60 61
AE6 459891171 2805423005 60 61
AE7 455803086 3272979034 60 61
chrUn 102925192 3736378846 60 61I can 7 processes in parallel
python misa_multiprocessing.py -g Avena_atlantica.fasta.gz -t 7-g genomefile（gz/fasta）
-t process (default=1)
-c chr name （default=all）
ls
Avena_atlantica.fasta.gz_second.tsv chr2A.fasta_second.fasta.statistics chr5A.fasta_second.fasta.statistics
Avena_atlantica.fasta.gz_second_all.fasta chr3A.fasta_second.fasta.statistics chr6A.fasta_second.fasta.statistics
chr1A.fasta_second.fasta.statistics chr4A.fasta_second.fasta.statistics chr7A.fasta_second.fasta.statistics
##########################################################################################
head -n 5 Avena_atlantica.fasta.gz_second.tsv
ID SSR nr. SSR type SSR size start end
chr1A:42775-43110 1 c (AC)6(AT)12 36 150 185
chr1A:174688-175102 1 c (TTG)5ttctgattctgattttgcaggaactgtgtcatcatctgcattagttgagcttgtcctgtcaacatctgctgtatctcgggagtga(TGT)5 115 150 264
chr1A:182555-182866 1 p2 (GA)6 12 150 161
chr1A:189505-189816 1 p2 (GA)6 12 150 161
##########################################################################################
head -n 5 Avena_atlantica.fasta.gz_second_all.fasta
>chr1A:42775-43110
AAATTTAATATTTTAGAATAATTTACATTGCTTACTCAAGCAAAGGGACTCAATCTCGTGAATGTTTAAACGCTACATGCTCAAGCTGTTGTCTTTTAGTACTTGTTCTATTTGCATTGCGTAAGTAGGACATCCTCATATCCACCGGAACACACACACACATATATATATATATATATATATATACACACATATATACATAAATTCAATTTGGTGATCATTTTTTTGCATATATGGATGATCTTCATAAATGACCACACTCTTTATCAAAATTTACCCTACTATCTATGGTATCATTTTAGAAAATTTGAAATAGTATTTCAAAATATTGGATA
>chr1A:174688-175102
CTTCGTCGGTGCAGCCAACAGTCACTAAGTCCTTATTCAGCGAACGTAACCAATCATTGGCTACCATTGGGTCAGTTGTTCCAGAGAACCTTGCAGGGCTTAGTTTCAAAAACCTGGTGAGCATATCATGTGCTGGAGGATTATTCTGATTGTTGTTGTTGTTGTTCTGATTCTGATTTTGCAGGAACTGTGTCATCATCTGCATTAGTTGAGCTTGTCCTGTCAACATCTGCTGTATCTCGGGAGTGATGTTGTTGTTGTTGTTTTGGTTGGGGTTGGCACGACGGGGAGGCATATGTTGGTTTGATAGGGATAAGTAATGATAGATAGGCATAAGGAAGTTCTGACACACAACTCAAAACAACCAAGTTCAATCAAACAATCAATCAATCAACAAGCAACTATCCACTTAAC
>chr1A:182555-182866Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003 Feb;106(3):411-22. doi: 10.1007/s00122-002-1031-0. Epub 2002 Sep 14. PMID: 12589540.
###设计引物链接https://github.com/yukaiquan/primer3-Multiprocessing