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SYNOPSIS

assembleAll.pl

Assembles raw reads into assembly and then predicts genes.

Software requirements

In version 2, Shovill was added and many requirements were added

  • Shovill - has many dependencies itself
    • BWA
    • Flash
    • Java
    • Lighter
    • Mash (before shovill 1.1.0)
    • KMC (in shovill 1.1.0)
    • Megahit (not used but checked when shovill runs)
    • pigz
    • Pilon
    • Samclip
    • Samtools
    • Seqtk
    • Skesa
    • Trimmomatic
    • Velvet (not used but checked when shovill runs)
  • CG-Pipeline
  • Prodigal
  • gfa_connector, part of the skesa package

Algorithm

Assembles genomes with Skesa, creates an assembly graph file with gfa_connector, predicts genes with prodigal, then produces assembly and gene prediction metrics. Contigs with length < 500 are not considered in the assembly metrics.

Outputs

Assemblies are found in SneakerNet/assemblies/[samplename]/*.fasta GFA graph file found in SneakerNet/assemblies/[samplename]/*.gfa Annotated assembly found in SneakerNet/assemblies/[samplename]/*.gbk

Table with columns

  • sample
  • genomeLength
  • CDS - number of coding sequences
  • N50
  • longestContig
  • numContigs
  • avgContigLength
  • assemblyScore - log(N50/numContigs * penalty) where a genome is penalized for being different than the expected genome length
  • minContigLength
  • expectedGenomeLength
  • kmer21 - a quantifier for how much 21-mers are duplicated. A marker for overassembly.
  • GC
  • effectiveCoverage - the number of mapped base pairs against the assembly. Will be lower than the coverage noted in readMetrics.

Starting with v2.5, four more output files are found in SneakerNet/assemblies/[samplename]/ but not included in the final report. These files are used to make the aforementioned combined metrics table.

  • predictionMetrics.tsv - gene prediction metrics such as CDS count
  • assemblyMetrics.tsv - N50, genomeLength, etc
  • depth.tsv.gz - samtools depth output: a three column file with contig, pos, depth of coverage
  • effectiveCoverage.tsv - contains effective coverage