dib-lab 2020-paper-sourmash-gather issues

dib-lab / 2020-paper-sourmash-gather

Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.

https://dib-lab.github.io/2020-paper-sourmash-gather

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sourmash benchmarking

#47 ctb opened 2 years ago
3
add acknowledgements and author contributions

#46 ctb opened 2 years ago
0
[MRG] add details on database used for tax bench

#45 ctb closed 2 years ago
0
[WIP] initial add of Rahman et al. reference

#44 ctb closed 2 years ago
1
[MRG] minor edits

#43 bluegenes closed 2 years ago
0
[MRG] upd name

#42 bluegenes closed 2 years ago
0
[MRG] typos on latest version

#41 taylorreiter closed 2 years ago
1
Figure 5 updates

#40 ctb opened 2 years ago
0
Figure 1 commentary and updates

#39 ctb opened 2 years ago
1
[MRG] add references to first paragraph of intro

#38 taylorreiter closed 2 years ago
0
more references to include

#37 ctb opened 2 years ago
0
discussion of taylor's suggestions from #35

#36 ctb opened 2 years ago
0
Suggested edits to the gather paper, and a few inline comments

#35 taylorreiter closed 2 years ago
1
add more set-cover references?

#34 ctb opened 2 years ago
0
[MRG] Update rootstock from manubot/rootstock

#33 ctb closed 2 years ago
0
merge master into main

#32 bluegenes closed 3 years ago
0
minor changes, x2

#31 ctb closed 3 years ago
0
what is our estimate of the number of total k-mers in genbank?

#30 ctb opened 3 years ago
1
figure out the right reference for min-set-cov greedy algorithm

#29 ctb opened 3 years ago
0
More writing.

#28 ctb closed 3 years ago
0
(re)visit sourmash issue around Scaled MinHash

#27 ctb opened 3 years ago
0
inspect kssd paper and see if we should reference

#26 ctb opened 3 years ago
0
cross-check discussion of Scaled MinHash with list in sourmash issue

#25 ctb opened 3 years ago
0
cross-check paper with list of sourmash use cases

#24 ctb opened 3 years ago
0
thought: many genomes is annoying.

#23 ctb opened 3 years ago
0
idea: is there value in mentioning min-set-cov as an idea for mappers?

#22 ctb opened 3 years ago
1
remember to cite modimizer

#21 ctb opened 3 years ago
0
reviewers to suggest

#20 ctb opened 3 years ago
6
reference: On the complexity of haplotyping a microbial community

#19 ctb opened 3 years ago
0
explore david's concerns

#18 ctb opened 3 years ago
1
collected items for another paper (on magsearch/etc) or papers

#17 ctb opened 3 years ago
1
min-set-cover references for genomics specifically

#16 ctb opened 3 years ago
2
how do we show "minimal" or close-to-minimal? how do we measure approximation?

#15 ctb opened 3 years ago
1
Update rootstock (as of 2020/11/30)

#14 luizirber closed 3 years ago
1
[WIP] LaTeX-heavy theoretical analysis method section

#13 luizirber closed 2 years ago
0
Remove the SBT/LCA stuff, as a trial.

#12 ctb closed 3 years ago
0
reference: Nucleotide-resolution bacterial pan-genomics with reference graphs

#11 ctb opened 3 years ago
0
can we fit david's analytical work on error bounds in this paper?

#10 ctb closed 3 years ago
3
leftover text from discussion

#9 ctb opened 3 years ago
0
leftover text from discussion

#8 ctb opened 3 years ago
0
leftover text from introduction

#7 ctb opened 3 years ago
0
stable hashing system - do we mention it in this paper, or save it?

#6 ctb closed 3 years ago
1
is Scaled MinHash still a sketch if it's unbounded in size?

#5 ctb opened 3 years ago
1
do we want to discuss gather & abundance?

#4 ctb closed 3 years ago
1
how do we showcase the accuracy of gather results, without using taxonomy?

#3 ctb closed 3 years ago
18
should we benchmark containment rather than similarity?

#2 ctb closed 3 years ago
3
Author information

#1 ctb closed 2 years ago
6