DSL2: preprocessing and mapping

[jfy133]

• FASTQC
• FASTP/ADAPTERREMOVAL
• FASTQC POST
• BWA ALN/BWA MEM/BOWTIE2/CIRCULAR MAPPING

Indexing

• BWA INDEX / BOWTIE2 INDEX (DSL2: single-genome indexing #926) / CIRCULARMAPPER
• SAMTOOLS FAIDX
• PICARD CREATESEQUENCEDICTIONARY

NEW

• Map by lane
• LEEHOM
• Multiple reference input

[jfy133]

Indexing Notes

• FASTA input only or TSV?
  • But what if need to specify chromosome?
  • Allow both?

    • If ending in {.fasta,.fna,.fas,.fa,.fasta.gz,.fna.gz,.fas.gz,.fa.gz} then just use that and make fake meta

    • If ending in .csv then make meta from TSV?

      ref_name,mt,fasta,fai,dict,mapindexdir,circulartarget,mt
      

  • May require patches to add meta? Or update meta?
  • Note: will need gunzip

Modules

• gunzip
• bwa index (requires update: add meta)
• bowtie2 build (requires update: add meta)
• circular mapper
• samtools faidx
• picard dictionary

[TCLamnidis]

Add mapAD?
NOTE: Cheristian mentioned in his Lab Seminar on 11/09/2023 that the map quality calculation between mapAD and BWA is a bit different. Might be good to note that when/if implementing mapAD

[TCLamnidis]

LEEHOM is not added, but everything else is.
Once MapAD get merged, this issue can close.
#1072