lyve-KSNP

A set of wrapper scripts for KSNP

Install

1. Clone with git
2. Update your PATH to the git directory

Updating

Use git pull -u

Usage

1. Create a ksnp database with lyve-manage-ksnp.pl

    Usage: lyve-manage-ksnp.pl *.fastq[.gz] -d database.fasta
    NOTE: you can also add fasta files that have already been converted; however you cannot add already-merged fasta files.
    -d database Of merged fastas, produced by ksnp executable merge_fasta_reads
                The database can also be a blank or nonexistant file that this
                script can create.
    --action indicates one of the following: add, add-assemblies, remove, repair, query. Default: query
      add:            add reads
      add-assemblies: add assembly
      remove:         remove entry
      repair:         recreate the ksnp fasta file index files
      query:          find out if an entry is present
    -t tmp/
   

2. Run KSNP with lyve-ksnp.pl

      Usage: lyve-ksnp.pl -d database.fasta -o outdir/ -t tmpdir/
      -kmerlength kmer length (default: 25)
      -keep to keep temporary files
      -q qsubxopts Any extra option you want to pass to qsub, e.g. -q '-q long.q'
   

Output files

1. The fasta file that you specify in lyve-manage-ksnp.pl, e.g., db.fasta
2. The database files for Lyve-KSNP
3. db.fasta.reads: the raw reads filenames that KSNP needs
4. db.fasta.assemblies: the finished assemblies filenames that KSNP needs
5. db.fasta.index: the index file that Lyve-KSNP needs
6. db.fasta.locked: This zero-byte file will appear when running Lyve-KSNP to avoid concurrency
7. out/ The KSNP output directory