Shasta assembly summary

Shasta version

Shasta Release 0.11.1

Reads used in this assembly

Read representation	1 (RLE)
Minimum read length	200
Number of reads	1706664
Number of read bases	5560477726
Average read length	3258
Read N50	5563
Number of run-length encoded bases	3890327243
Average length ratio of run-length encoded sequence over raw sequence	0.6996
Number of reads flagged as palindromic by self alignment	119421
Number of reads flagged as chimeric	621

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	1871	250931
Reads discarded on input because they contained repeat counts greater than 255	72	322361
Reads discarded on input, total	1943	573292
Fraction of reads discarded on input over total present in input files	0.001137	0.0001031

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	379210669
Total number of markers on all reads, both strands	758421338
Average number of markers per raw base	0.0682
Average number of markers per run-length encoded base	0.09748
Average base offset between markers in raw sequence	14.66
Average base offset between markers in run-length encoded sequence	10.26
Average base gap between markers in run-length encoded sequence	-3.741

Alignments

Number of alignment candidates found by the LowHash algorithm	40390
Number of good alignments	36638
Number of good alignments kept in the read graph	27757

Alignment criteria actually used for creation of the read graph

minAlignedMarkerCount	25
minAlignedFraction	0.475
maxSkip	21
maxDrift	10
maxTrim	80

Read graph

Number of vertices	3413328
Number of edges	55514

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	1678505	5365926349
Non-isolated reads	28159	194551377
Isolated reads fraction	0.9835	0.965
Non-isolated reads fraction	0.0165	0.03499

Marker graph

Total number of vertices	222694
Total number of edges	302514
Number of vertices that are not isolated after edge removal	201106
Number of edges that were not removed	199368

The marker graph contains both strands.

Assembly graph

Number of vertices	3502
Number of edges	1764
Number of edges assembled	882

The assembly graph contains both strands.

Assembled segments ("contigs")

Number of segments assembled	882
Total assembled segment length	2444894
Longest assembled segment length	10877
Assembled segments N₅₀	4170

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)	240.9
Elapsed time (minutes)	4.014
Elapsed time (hours)	0.0669
Average CPU utilization	0.204
Peak virtual memory utilization (bytes)	37619863552
Number of threads used	60
Total number of virtual CPUs available	20
Total physical memory available (bytes)	270208720896