README.md

Overlap Graphs

To prepare libraries for this pipeline:

1. poretools fasta --type 2D <path/to/base/called/reads/> > <name.fasta>
2. bwa mem -x on2d <indexed_reference.fasta> <name.fasta> | samtools view -bS - | samtools sort -o <name.sorted.bam> -
3. samtools depth <name.sorted.bam> > <name.coverage>

• head <name.coverage> # This finds the name of the 'chromosome'; there may be >1.

4. awk '$1 == "<chromosomename>" {print $0}' <name.coverage> > chr1.coverage
5. Repeat for paired library
6. Fill in and into pool1 and pool2 in depth_coverage.R
7. Stats acquired using poretools stats <path/to/base/called/reads

Reported p20 and p40 values represent percentage of the Zika genome which has at coverage of at least 20/40 reads, respectively.

Overlap graphs and stats on pass libraries

NB01-NB07 Overlap

p20: 0.9702 p40: 0.9671

	NB01	NB07
total reads	9729	7530
total base pairs	5225355	3992373
mean	537.09	530.20
median	547	550
min	213	201
max	1781	1827
N25	580	577
N50	552	555
N75	520	508

NB02-NB08 Overlap

p20: 0.8412 p40: 0.7145

	NB02	NB08
total reads	8277	6462
total base pairs	4402300	3463771
mean	531.87	536.02
median	541	554
min	176	213
max	1721	1309
N25	570	578
N50	544	558
N75	518	523

NB03-NB09 Overlap

p20: 0.6571 p40: 0.5022

	NB03	NB09
total reads	3618	4845
total base pairs	1888020	2638147
mean	521.84	544.51
median	531	557
min	265	277
max	1662	1696
N25	562	579
N50	535	561
N75	501	531

NB04-NB010 Overlap

p20: 0.9384 p40: 0.9087

	NB04	NB10
total reads	12381	7224
total base pairs	6450344	3853127
mean	520.99	533.38
median	538	550
min	192	207
max	1939	2260
N25	575	577
N50	544	555
N75	498	514

NB05-NB11 Overlap

p20: 0.9066 p40: 0.8737

	NB05	NB11
total reads	13479	9558
total base pairs	7376656	5043864
mean	547.27	527.71
median	551	549
min	183	168
max	1846	1874
N25	578	578
N50	554	555
N75	530	504

NB06-NB12 Overlap

p20: 0 p40: 0

	NB06	NB12
total reads	81	33
total base pairs	28077	16649
mean	346.63	504.52
median	323	517
min	145	322
max	600	596
N25	518	574
N50	341	546
N75	302	476