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sra-human-scrubber
An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
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Docker image is missing ps
#31
maxlcummins
opened
1 month ago
3
HRRT on ONT data
#30
cimendes
closed
4 months ago
2
How to tell if this has been run on a sample
#29
mbhall88
opened
10 months ago
2
print version # and exit option
#28
chrisgulvik
opened
11 months ago
0
human kmer present in Escherichia coli reference genome
#27
mikelchtermans
closed
11 months ago
4
Dockerized version unresponsive on Intel and Apple Silicon macs
#26
dhoconno
opened
1 year ago
1
Memory usage
#25
bede
closed
1 year ago
5
Can't use stdin and keep spots
#24
mbhall88
closed
1 year ago
3
interleaved reads are not paired anymore after scrubbing with -x option
#23
Bio-finder
closed
1 year ago
11
Out of space (/tmp) during fastq_to_fasta.py
#22
accopeland
closed
1 year ago
1
Source code?
#21
accopeland
closed
2 years ago
3
custom database
#20
manolis2023
closed
1 year ago
1
SRAB-42, correct the option output
#19
multikengineer
closed
3 years ago
0
Srab 42 fix help
#18
multikengineer
closed
3 years ago
0
Srab 44 merge
#17
multikengineer
closed
3 years ago
1
Srab 44 - k florek changes
#16
multikengineer
closed
3 years ago
5
fixed path
#15
k-florek
closed
3 years ago
8
Best method to determine current sra-human-scrubber version?
#14
rpetit3
closed
1 year ago
3
Sra 10422 add license
#13
multikengineer
closed
3 years ago
0
Is there a protocol for creating a custom database?
#12
rpetit3
closed
3 years ago
2
Please add a license
#11
rpetit3
closed
3 years ago
2
Allow DB location to be specified
#10
pvanheus
closed
3 years ago
3
Option to specify the number of cores used?
#9
rpetit3
closed
2 years ago
9
add gzip support for scrubber
#8
rpetit3
closed
3 years ago
1
Mirroring Docker container on Quay.io?
#7
rpetit3
closed
3 years ago
3
Paired-end Reads
#6
bioinfoMMS
closed
3 years ago
7
please version the database
#5
pvanheus
closed
2 years ago
2
Cannot process .gz files
#4
kevinlibuit
closed
3 years ago
9
Some lines left without quality scores
#3
kevinlibuit
closed
3 years ago
1
There is no code here.
#2
kevinlibuit
closed
3 years ago
1
Source release?
#1
olsonanl
closed
3 years ago
6