Assembly

Input Reads

../20171018_oly_pacbio.trimmedReads.fasta.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	723260 reads (3513500524 bp)
FASTA	0 reads (0 bp) were short and not loaded
FASTQ	0 reads (0 bp)
FASTQ	0 reads (0 bp) were short and not loaded
723260 reads (3513500524 bp) loaded, 0 reads (0 bp) skipped, 0 warnings

Final Store

unitigging/20171018_oly_pacbio.gkpStore
readsLoaded	723260 reads (3513500524 bp)
readsSkipped	0 reads (0 bp) (read was too short)
warnings	0 warnings (invalid base or quality value)

Read Length Histogram

k-Mer Counts

Histogram for k=22 with 3498312064 mers, 1104950071 distinct mers and 725696616 single-copy mers. Largest count is 1180657.

Overlaps

Category	Reads	%	Read Length			Feature Size or Coverage			Analysis
middle-missing	1699	0.23	5836.53	±	3147.72	626.11	±	728.33	bad trimming
middle-hump	18543	2.56	5119.56	±	2621.57	111.13	±	322.64	bad trimming
no-5-prime	38530	5.33	5943.75	±	2512.95	78.06	±	283.14	bad trimming
no-3-prime	33037	4.57	5855.59	±	2636.73	88.36	±	302.87	bad trimming
low-coverage	266450	36.84	4000.00	±	2281.65	4.18	±	1.93	easy to assemble, potential for lower quality consensus
unique	63758	8.82	3557.46	±	1987.19	19.17	±	8.73	easy to assemble, perfect, yay
repeat-cont	21849	3.02	3844.08	±	2434.09	384.74	±	454.87	potential for consensus errors, no impact on assembly
repeat-dove	102	0.01	10318.17	±	3376.82	164.14	±	117.96	hard to assemble, likely won't assemble correctly or even at all
span-repeat	100087	13.84	6237.15	±	2208.44	2815.30	±	2079.79	read spans a large repeat, usually easy to assemble
uniq-repeat-cont	142305	19.68	5250.49	±	2081.27				should be uniquely placed, low potential for consensus errors, no impact on assembly
uniq-repeat-dove	30539	4.22	7130.44	±	2324.91				will end contigs, potential to misassemble
uniq-anchor	1670	0.23	7121.67	±	2410.15	2457.85	±	1879.88	repeat read, with unique section, probable bad read

Overlap Error Adjustment

Unitigs

Overlaps

Loaded all overlaps for 0 reads.
Loaded 0 overlaps in total.

Edges

Constructing unitigs using overlaps of at most this fraction error:
0.03160000 +- 0.01220000 = 0.14012632 = 14.012632% (median absolute deviation)
0.03332694 +- 0.01640734 = 0.13177098 = 13.177098% (standard deviation)

INITIAL EDGES
533582 reads are contained.
37621 reads are singleton.
78018 reads are spur (70361 have a mutual best edge).
74039 reads form the backbone (1596 have no mutual best edges; 12901 have one; 59542 have both).

FILTERING
0 reads have a suspicious overlap pattern.
0 had one high error rate edge filtered; 0 had both.
11431 had one size incompatible edge filtered; 1113 had both.

FINAL EDGES
533582 reads are contained.
78881 reads are singleton.
79278 reads are spur (24181 have a mutual best edge).
31519 reads form the backbone (5493 have no mutual best edges; 2189 have one; 23837 have both).

Assembly

Input Reads

Final Store

Read Length Histogram

k-Mer Counts

Overlaps

Overlap Error Adjustment

Unitigs

Overlaps

Edges

Initial Tig Sizes

Final Tig Sizes

Consensus

Final Outputs