Assembly

Input Reads

../oly_pacbio_.trimmedReads.fasta.gz
Parameterspreset = N/A
defaultQV = 20
isNonRandom = false
removeDuplicateReads = true
finalTrim = true
removeSpurReads = true
removeChimericReads = true
checkForSubReads = true
FASTA531895 reads (2350716406 bp)
0 reads (0 bp) were short and not loaded
FASTQ0 reads (0 bp)
0 reads (0 bp) were short and not loaded
531895 reads (2350716406 bp) loaded, 0 reads (0 bp) skipped, 0 warnings

Final Store

unitigging/oly_pacbio_.gkpStore
readsLoaded531895 reads (2350716406 bp)
readsSkipped0 reads (0 bp) (read was too short)
warnings0 warnings (invalid base or quality value)

Read Length Histogram

k-Mer Counts

Histogram for k=22 with 2339546611 mers, 568199193 distinct mers and 313362000 single-copy mers. Largest count is 782346.

Overlaps

CategoryReads%Read LengthFeature Size or CoverageAnalysis
middle-missing 11020.215241.84±2637.76606.03±733.65bad trimming
middle-hump 179533.384380.76±2307.8972.66±244.36bad trimming
no-5-prime 324886.115377.39±2220.0759.58±232.03bad trimming
no-3-prime 241534.545118.51±2340.5576.09±257.30bad trimming
low-coverage 21224439.903616.23±2028.014.50±1.93easy to assemble, potential for lower quality consensus
unique 455438.563448.74±1886.8619.99±9.20easy to assemble, perfect, yay
repeat-cont 125382.363941.61±2503.35346.20±349.73potential for consensus errors, no impact on assembly
repeat-dove 530.0111933.47±3586.68205.70±113.55hard to assemble, likely won't assemble correctly or even at all
span-repeat 7142713.435827.68±1924.042924.15±1965.97read spans a large repeat, usually easy to assemble
uniq-repeat-cont 9438517.754896.24±1943.10should be uniquely placed, low potential for consensus errors, no impact on assembly
uniq-repeat-dove 155632.936708.05±2077.58will end contigs, potential to misassemble
uniq-anchor 7550.146895.14±2378.842258.25±1873.62repeat read, with unique section, probable bad read

Overlap Error Adjustment

Unitigs

Overlaps

Loaded all overlaps for 531895 reads.
Loaded 14742398 overlaps in total.

Edges

Constructing unitigs using overlaps of at most this fraction error:
0.02010000 +- 0.00680000 = 0.08059008 = 8.059008% (median absolute deviation)
0.02092904 +- 0.00922292 = 0.07626658 = 7.626658% (standard deviation)

INITIAL EDGES
396475 reads are contained.
34396 reads are singleton.
59357 reads are spur (55103 have a mutual best edge).
41667 reads form the backbone (1114 have no mutual best edges; 5679 have one; 34874 have both).

FILTERING
0 reads have a suspicious overlap pattern.
0 had one high error rate edge filtered; 0 had both.
4934 had one size incompatible edge filtered; 644 had both.

FINAL EDGES
396475 reads are contained.
69228 reads are singleton.
50729 reads are spur (15435 have a mutual best edge).
15463 reads form the backbone (2781 have no mutual best edges; 825 have one; 11857 have both).

Initial Tig Sizes

Final Tig Sizes

Consensus

Final Outputs