satminer

satMiner: A Toolkit to NGS satellite DNA mining and analysis

##Installation

• Copy script to your binaries folder.
• Dependencies:
  • BioPython http://biopython.org/wiki/Main_Page
  • RepeatMasker http://www.repeatmasker.org/RMDownload.html
  • seqTK https://github.com/lh3/seqtk
  • DeconSeq http://deconseq.sourceforge.net
  • BLAT http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/
  • Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic

##1. satDNA mining

###1a. Preparing sequences to RepeatExplorer

There is not a number of paired reads to start. You can try with 100000 or 200000. You should also indicate the minimum quality and the minimum length. For example if you are using Illumina PE 2x100 reads, you can try 20 and 100, respectively.

$ rexp_prepare.py NumberOfPairedReads LibraryA_1.fastq LibraryA_2.fastq MinQual MinLen

###1b. Run RepeatExplorer

Run RepeatExplorer with default options.

###1c. Get contigs

Uncompress RepeatExplorer's output and go to the "clusters" folder. Get a list with the name of the contigs representing a half of the number of the cluster reads reads.

$ cd seqClust/clustering/clusters
$ rexp_get_contigs.py

Since clusters with few number of reads are difficult to distinguish as satDNA clusters, we select a half of the clusters and we then extract the sequences as a FASTA file:

$ extract_seq.py FastaFile List

###1d. Run DeconSeq

$ deconseq_run.py ListOfFastaFiles Reference Threads

###1e. Prepare filtered reads to RepeatExplorer Usually, we recommend to duplicate the number of reads.

$ rexp_prepare_deconseq.py NumberOfPairedReads LibraryA_clean_1.fastq LibraryA_clean_2.fastq

You will then get a FASTA file to run again RepeatExplorer, so continue with step 1b.

##2. satDNA analysis

###2a. Homology among consensus sequences

$ rm_homology.py FastaFile

###2b. Intragenomic variation

$ rm_getseq.py FastaFile RepeatMaskerOut [LenMinimum]

Optionally:

$ sat_cutter.py AlignedFastaFile

###2c. Abundance and divergece

$ repeat_masker_run_big.py ListOfFastaFiles FastaReference NumberOfThreads

Pattern File with tab-separated names:

Sat-01A	Sat-01A
Sat-02A Sat-02A
Sat-02B	Sat-02A

Running script

$ sat_subfam2fam.py AlignFile PatternFile