Galaxy |

Shovill (version 1.1.0+galaxy2)

Input reads type, collection or single library:

Select 'paired end' for a single library or 'collection' for a paired end collection

Forward reads (R1):

The file of forward reads in FASTQ format

Reverse reads (R2):

The file of reverse reads in FASTQ format

Trim reads:

Use Trimmomatic to remove common adaptors first (default: OFF)

Assembler to use:

Which assembler would you like shovill to use, default is Spades

Advanced options

Advanced options 0

Output log file?:

Return the Shovill log file as part of the output. Default is on

Synopsis: Faster de novo assembly pipeline for Illumina paired end reads based around Spades

Details and options: - Takes paired end Illumina fastq reads - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF) - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output - Assembler: Which assembler should shovill use from: Skesa, Megahit, Velvet or Spades. Spades is the default.

Advanced options: - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d') - Depth: Sub-sample the reads to this depth. Disable with Depth: 0 (default: 100) - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '') - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON) - Keep the bam files : Enable to keep mapped files from bwa in the post assembly correction (default: OFF) - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0) - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2) - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')

Documentation can be found at Torsten Seemann site.