Sus scrofus samples with high or low virus abundance

[taltman]

I forget who exactly mentioned this, but there are known samples with high levels of coronavirus, and those with low abundance. Can someone please update the Assembly wiki page with the context & accessions? Thanks! https://github.com/ababaian/serratus/wiki/Serratus-Assembly

[ababaian]

Pig high coverage samples matching PEDV

SRR10829958
SRR10829957
SRR10829954
SRR10829953
SRR10829952
SRR10829951

Pig low coverage samples matching IBV

SRR10951665.summary:acc=pan_genome;hits=866;len=30000;depth=2.92;pctid=95.4;tax=?;cov=1.0000;coverage=...............................O;desc=Pan-genome;
SRR10951664.summary:acc=pan_genome;hits=1142;len=30000;depth=3.84;pctid=97.8;tax=?;cov=1.0000;coverage=OoOOOOooo.OoOoooooooooooOooooOOO;desc=Pan-genome;
SRR10951663.summary:acc=pan_genome;hits=746;len=30000;depth=2.51;pctid=95.1;tax=?;cov=1.0000;coverage=o..oo..............o........oooO;desc=Pan-genome;
SRR10951662.summary:acc=pan_genome;hits=1182;len=30000;depth=3.98;pctid=98.1;tax=?;cov=1.0000;coverage=OooOOOOooOOoOOoOOooOoooOooOoOOOO;desc=Pan-genome;
SRR10951661.summary:acc=pan_genome;hits=677;len=30000;depth=2.28;pctid=94.8;tax=?;cov=1.0000;coverage=............................o..O;desc=Pan-genome;
SRR10951660.summary:acc=pan_genome;hits=1047;len=30000;depth=3.52;pctid=97.9;tax=?;cov=1.0000;coverage=OOoOOO.oooOOooooooooooOOOOOoOOOO;desc=Pan-genome;
SRR10951659.summary:acc=pan_genome;hits=1058;len=30000;depth=3.56;pctid=94.6;tax=?;cov=1.0000;coverage=ooooooooo.oooooOoo.ooooo.oooOoOO;desc=Pan-genome;
SRR10951658.summary:acc=pan_genome;hits=1982;len=30000;depth=6.67;pctid=98.1;tax=?;cov=1.0000;coverage=OOOOOOOOOoOoOOOOOooOOoOOooOOOOOo;desc=Pan-genome;
SRR10951657.summary:acc=pan_genome;hits=1139;len=30000;depth=3.83;pctid=94.0;tax=?;cov=1.0000;coverage=Ooooooooooo.ooOooo.ooooo.oooOoOO;desc=Pan-genome;
SRR10951656.summary:acc=pan_genome;hits=2361;len=30000;depth=7.95;pctid=98.2;tax=?;cov=1.0000;coverage=OOOOOOooOoOoOoooOooOooOOooOOOOOo;desc=Pan-genome;
SRR10951655.summary:acc=pan_genome;hits=1011;len=30000;depth=3.4;pctid=94.7;tax=?;cov=1.0000;coverage=oo.o.o......o..o...oo.oo..o.oooO;desc=Pan-genome;
SRR10951654.summary:acc=pan_genome;hits=1830;len=30000;depth=6.16;pctid=98.0;tax=?;cov=1.0000;coverage=OoOOOOooooOoooooOooOOoOOooOoOOOo;desc=Pan-genome;

[taltman]

@rcedgar I noticed that you closed this issue. Let's use the Serratus Assembly Github Project work-flow, where tasks that are completed are reviewed before they get marked as done & closed. For example, I need to move this content to the wiki, and then it is closed. Otherwise, people have to fish around closed issues trying to find snippets of information. Thanks! For your convenience, here is a link to the Project view: https://github.com/ababaian/serratus/projects/2

[rcedgar]

FYI, nothing against the work-flow approach but I don't understand it and and don't have time to learn it right now.

[taltman]

All you have to do is drag the "card" that represents the issue from the "TODO" or "In Progress" column to the "Review in progress" column. Not exactly particle physics. :-p

[ababaian]

How about for issues. If you open it. You close it. Or we @ bump you to close it if you're slacking

[rcedgar]

That sounds like good etiquette, probably I shouldn't have closed @taltman's issue; I was trying to cut down on the number of open issues,

[taltman]

@ababaian I like that protocol! I will document it on the wiki as part of closing this issue. Another alternative is to reassign the issue to the person that you want to review the work, to sign off that it's complete and then can close the issue. @rcedgar No worries! We're figuring out how to pilot this plane as we're building it. :-)

[ababaian]

Benchmark defined in #130 now