Shasta assembly summary

Shasta version

Shasta Release 0.11.1

Reads used in this assembly

Read representation	0 (Raw - no RLE)
Minimum read length	10000
Number of reads	10550267
Number of read bases	248580511297
Average read length	23561
Read N50	26008
Number of reads flagged as palindromic by self alignment	81768
Number of reads flagged as chimeric	175524

Reads discarded on input are not included in the above table (see below).
See ReadLengthHistogram.csv and Binned-ReadLengthHistogram.csv for details of the read length distribution of reads used in this assembly.

Reads discarded on input

	Reads	Bases
Reads discarded on input because they contained invalid bases	0	0
Reads discarded on input because they were too short	0	0
Reads discarded on input because they contained repeat counts greater than 255	0	0
Reads discarded on input, total	0	0
Fraction of reads discarded on input over total present in input files	0	0

Base counts in the above table are raw sequence bases.
Here and elsewhere, "raw" refers to the original read sequence, as opposed to run-length encoded sequence.

Marker k-mers

Length k of k-mers used as markers	14
Total number of k-mers	6377292
Number of k-mers used as markers	638031
Fraction of k-mers used as markers	0.1

In the above table, all k-mer counts only include run-length encoded k-mers, that is, k-mers without repeated bases.

Markers

Total number of markers on all reads, one strand	24715094575
Total number of markers on all reads, both strands	49430189150
Average number of markers per base	0.09942
Average base offset between markers	10.06
Average base gap between markers	-3.942

Alignments

Number of alignment candidates found by the LowHash algorithm	1092329378
Number of good alignments	251919107
Number of good alignments kept in the read graph	111022912

Alignment criteria actually used for creation of the read graph

minAlignedMarkerCount	400
minAlignedFraction	0.7
maxSkip	20
maxDrift	10
maxTrim	20

Read graph

Number of vertices	21100534
Number of edges	222045824

The read graph contains both strands. Each read generates two vertices.
Isolated reads in the read graph don't contribute to the assembly. See the table below for a summary of isolated reads in the read graph. Each isolated read corresponds to two isolated vertices in the read graph, one for each strand.

	Reads	Bases
Isolated reads	769176	18530655236
Non-isolated reads	9781091	230049856061
Isolated reads fraction	0.07291	0.07455
Non-isolated reads fraction	0.9271	0.9255

Marker graph

Total number of vertices	965903914
Total number of edges	2020368672
Number of vertices that are not isolated after edge removal	779625680
Number of edges that were not removed	780023100

The marker graph contains both strands.

Assembly graph

Number of vertices	61932
Number of edges	96964
Number of edges assembled	48482

The assembly graph contains both strands.

Assembled segments ("contigs")

Number of segments assembled	48482
Total assembled segment length	4112767228
Longest assembled segment length	5547829
Assembled segments N₅₀	695621

Shasta uses GFA terminology (segment instead of the most common contig). A contiguous section of assembled sequence can consist of multiple segments, for example in the presence of heterozygous bubbles.
See AssemblySummary.csv for lengths of assembled segments.

Performance

Elapsed time (seconds)	5.35e+04
Elapsed time (minutes)	891.7
Elapsed time (hours)	14.86
Average CPU utilization	0.2037
Peak virtual memory utilization (bytes)	1847776256000
Number of threads used	40
Total number of virtual CPUs available	128
Total physical memory available (bytes)	2151687938048