specialtigs

Assembler-specific proteins (from cdhit and/or mmseqs2 analysis)

• tax. class. w/ kaiju (already part of the pipeline)
• mmseqs2 analysis (outside of the main pipeline)
• collect stat.s about gene length, cluster size etc.
• example: cov. plots for a specific contig from a LR assembly highlighting uniq. genes

changed milestone to %Analyses

added Analysis Investigation labels

changed the description

marked the checklist item mmseqs2 analysis (outside of the main pipeline) as completed

Removed mmseqs2 - other analyses are more important.

marked the checklist item collect stat.s about gene length, cluster size etc. as completed

mentioned in commit f49767ce

changed the description

marked the checklist item example: cov. plots for a specific contig from a LR assembly highlighting uniq. genes as completed

mentioned in commit 1257fcdb

mentioned in commit 1600fdd4

Example:

• SR-polished LR assembly flye + racon(SR), contig contig_446
• "unique" genes are those not found in SR assembly metaspades (cdhit results)
• metaT/metaG (SR) coverage plots

lr_flye_sr_contig_446.pdf

Looked at contig_446_31 and contig_446_34

• both unique, complete, GC content. ca. 0.6
• BLASTp results (NCBI): WP_114000182.1, WP_114000184.1
• their neighbors, contig_446_30 and contig_446_35 have a match in metaspades assembly
  • but the matched genes are on short contigs, i.e. being the last gene on the contig
  • assumption: the unique genes do not have a match because the SR assembler was not able to reconstruct these regions

closed