The alignment pipeline aligns FASTA or FASTQ or FAST5 files to a reference.
Input: FASTA/FASTQ/FAST5 file & reference Output: Sorted BAM file
Tests: - # mapped/ # unmapped - median/mean coverage - time to run - histogram of alignment lengths - coverage plots
This pipeline takes an alignment and post-processes it, e.g. with the aim of improving SNP or indel calling sensitivity/specificity.
Input: Sorted BAM file Output: Sorted BAM file
Tests: - ??
This pipeline takes results from alignment or alignment corrector and produces a consensus output.
Input: FASTA file & reference Output: VCF file
Tests: - number of bases correct - number of bases called - number of bases incorrect (SNPs, indels)
The reference is mutated, e.g. 0.1%, 1%, 5% nucleotide divergence and a consensus is produced.
Tests: - truth table - ROC curves
De novo assembly using Illumina reads as guide.
Tests: - QUAST output
Nanopore only assembly.
Reads are corrected by Illumian reads.
Reads are corrected, e.g. by a statistical model or by FAST5 squiggles.