Assembly

Input Reads

../asm.trimmedReads.fasta.gz
Parameters	preset = N/A
	defaultQV = 20
	isNonRandom = false
	removeDuplicateReads = true
	finalTrim = true
	removeSpurReads = true
	removeChimericReads = true
	checkForSubReads = true
FASTA	339 reads (1929638 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
339 reads (1929638 bp) loaded, 0 reads (0 bp) skipped, 0 warnings

Final Store

unitigging/asm.gkpStore
readsLoaded	339 reads (1929638 bp)
readsSkipped	0 reads (0 bp) (read was too short)
warnings	0 warnings (invalid base or quality value)

Read Length Histogram

Image 'unitigging/asm.gkpStore/readlengths' not found.

k-Mer Counts

Image 'unitigging/0-mercounts/asm.ms22.histogram' not found.

Overlaps

Category	Reads	%	Read Length			Feature Size or Coverage			Analysis
middle-missing	0	0.00	0.00	±	0.00	0.00	±	0.00	bad trimming
middle-hump	0	0.00	0.00	±	0.00	0.00	±	0.00	bad trimming
no-5-prime	1	0.29	7612.00	±	0.00	0.00	±	0.00	bad trimming
no-3-prime	1	0.29	8709.00	±	0.00	0.00	±	0.00	bad trimming
low-coverage	0	0.00	0.00	±	0.00	0.00	±	0.00	easy to assemble, potential for lower quality consensus
unique	306	90.27	5598.83	±	1960.36	33.30	±	6.94	easy to assemble, perfect, yay
repeat-cont	0	0.00	0.00	±	0.00	0.00	±	0.00	potential for consensus errors, no impact on assembly
repeat-dove	0	0.00	0.00	±	0.00	0.00	±	0.00	hard to assemble, likely won't assemble correctly or even at all
span-repeat	5	1.47	7172.60	±	1940.10	586.60	±	264.40	read spans a large repeat, usually easy to assemble
uniq-repeat-cont	20	5.90	5832.85	±	1319.04				should be uniquely placed, low potential for consensus errors, no impact on assembly
uniq-repeat-dove	6	1.77	7925.67	±	1675.65				will end contigs, potential to misassemble
uniq-anchor	0	0.00	0.00	±	0.00	0.00	±	0.00	repeat read, with unique section, probable bad read

Overlap Error Adjustment

Unitigs

Overlaps

Loaded all overlaps for 339 reads.
Loaded 19168 overlaps in total.

Edges

Constructing unitigs using overlaps of at most this fraction error:
0.00730000 +- 0.00300000 = 0.03398680 = 3.39868% (median absolute deviation)
0.01004243 +- 0.00749952 = 0.05503952 = 5.503952% (standard deviation)

INITIAL EDGES
279 reads are contained.
0 reads are singleton.
2 reads are spur (2 have a mutual best edge).
58 reads form the backbone (1 have no mutual best edges; 2 have one; 55 have both).

FILTERING
0 reads have a suspicious overlap pattern.
9 had one high error rate edge filtered; 2 had both.
3 had one size incompatible edge filtered; 0 had both.

FINAL EDGES
278 reads are contained.
1 reads are singleton.
4 reads are spur (2 have a mutual best edge).
56 reads form the backbone (3 have no mutual best edges; 2 have one; 51 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