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NCBI-Hackathons
/
STREAMclean
A simple command line tool to map SRA reads with high accuracy
MIT License
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3
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Bump urllib3 from 1.22 to 1.26.5
#38
dependabot[bot]
opened
3 years ago
0
Bump requests from 2.18.4 to 2.20.0
#37
dependabot[bot]
opened
5 years ago
0
Bump urllib3 from 1.22 to 1.24.2
#36
dependabot[bot]
closed
3 years ago
1
Test and update documentation around comma-separated list for taxa
#35
kbshimmyo
opened
6 years ago
1
Human and mouse Plots
#34
belfordak
closed
6 years ago
1
added contributing.md
#33
gedankenstuecke
closed
6 years ago
0
upload plots to help with alignment score threshold
#32
arvkevi
closed
6 years ago
1
The magicblast path is fixed and not portable
#31
hsiaoyi0504
opened
6 years ago
4
check presence of -s
#30
gedankenstuecke
closed
6 years ago
0
check that readme does not contain old name
#29
gedankenstuecke
closed
6 years ago
1
rename repo to STREAMclean (admin may have to do this)
#28
kbshimmyo
closed
6 years ago
2
create outdir if it doesn't exist
#27
arvkevi
closed
6 years ago
2
add Dockerfile
#26
stevetsa
opened
6 years ago
1
Sanitize input directory specifications
#25
kbshimmyo
opened
6 years ago
0
magicblast score threshold
#24
arvkevi
closed
6 years ago
0
edit readme to include workflow.
#23
gedankenstuecke
closed
6 years ago
0
Scores are now properly summed up across all alignments
#22
gedankenstuecke
closed
6 years ago
0
Validate that -s args is provided (required)
#21
kbshimmyo
closed
6 years ago
0
Housekeeping of repo
#20
kbshimmyo
opened
6 years ago
0
File format flag is missing
#19
gedankenstuecke
opened
6 years ago
0
[RDY] started adding blast processing to wrapper
#18
gedankenstuecke
closed
6 years ago
1
Score threshold is missing
#17
gedankenstuecke
closed
6 years ago
1
Should we use -R {reference/representative} in call to ncbi-genome-download?
#16
kbshimmyo
opened
6 years ago
2
Add download/db-construction size/time estimation module
#15
kbshimmyo
opened
6 years ago
2
streamin_magicblast can now in/exclude (closes #13)
#14
gedankenstuecke
closed
6 years ago
0
Filtering python script only discards, doesn't keep right now
#13
gedankenstuecke
closed
6 years ago
0
Add workflow graph
#12
gedankenstuecke
closed
6 years ago
0
Include magicblast & processing in wrapper
#11
gedankenstuecke
closed
6 years ago
1
Refactoring idea: one taxaList and a flag for the include/exclude switch
#10
kbshimmyo
opened
6 years ago
1
Update mapper_wrapper.sh
#9
gedankenstuecke
closed
6 years ago
0
Options for cutoff
#8
gedankenstuecke
closed
6 years ago
0
On passing the "--taxid 199310 bacteria" through to ncbi-genome-download
#7
kbshimmyo
closed
6 years ago
0
SRA number still has to become an argument, yes?
#6
kbshimmyo
closed
6 years ago
1
Output directory arg isn't currently doing anything
#5
kbshimmyo
closed
6 years ago
1
made the output script do fastq too
#4
gedankenstuecke
closed
6 years ago
0
Web portal - user to download the output file
#3
kbshimmyo
opened
6 years ago
1
Nice to: validate input to require exactly one of d, e, i options
#2
kbshimmyo
closed
6 years ago
0
usage function's wording
#1
kbshimmyo
closed
6 years ago
0