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bede
/
hostile
Precise host read removal
MIT License
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Update pinned aligner versions
#44
bede
opened
2 weeks ago
0
Dockerfile fails: process "/bin/sh -c mamba env update -n base -f hostile/environment.yml" did not complete successfully
#43
dterumalai
closed
2 weeks ago
3
Hostile with no options classifying different than --invert
#42
jannikseidelQBiC
opened
2 weeks ago
3
Allow adding of Illumina Casava 1.8 format entry to fastq headers
#41
charlesfoster
opened
3 weeks ago
2
Feat/refactor to hostile eit
#40
JDhillonEIT
closed
2 months ago
1
Automatically generate and cache minimap2 indexes to eliminate redundant indexing overhead
#39
bede
opened
3 months ago
0
Mode: paired short read (Bowtie2) fails when index is provided as reference fasta file
#38
Rohit-Satyam
closed
3 months ago
1
Allow remote index repository to be overridden
#37
bede
opened
4 months ago
0
Selection of appropriate reference genomes (indexes)
#36
DrYoungOG
opened
4 months ago
4
Support accepting stdin instead of a specific filepath for single ended data
#35
BioWilko
opened
5 months ago
2
Incorporating Single-End Short Read Data Support
#34
Ackia
closed
5 months ago
5
I think you can use --name (-n) on the mamba command line to override the environment name in the env file.
#33
bdklahn
closed
5 months ago
1
What's the best way to override the index download directory?
#32
bdklahn
closed
5 months ago
17
Suitable for metatranscriptomics?
#31
ym2877
closed
5 months ago
3
virus masked human genome
#30
xiaoli-dong
closed
8 months ago
5
Add versions and options to json log
#29
bede
closed
8 months ago
1
Allow non-default databases in cloud bucket to be downloaded on first run
#28
bede
closed
8 months ago
3
Regarding the choice of Reference genomes
#27
LilyAnderssonLee
closed
1 year ago
3
Refactor with more OOP
#26
bede
closed
8 months ago
1
Corrupted output if decontaminating more than one sample using Python API
#25
bede
closed
1 year ago
1
When 0 reads remain after decontamination, an invalid gzip file is created
#24
bede
closed
8 months ago
1
Validate scrubbed output in tests/CI
#23
bede
closed
1 year ago
1
Add completion message on stderr
#22
bede
closed
1 year ago
1
Bowtie2 performance suffers when using many threads in some conditions
#21
bede
closed
11 months ago
3
Discard partially downloaded indexes
#20
bede
closed
8 months ago
5
Make --debug useful
#19
bede
closed
1 year ago
1
Dockerise
#18
bede
closed
1 year ago
3
Skip checking presence of default ref/index if user supplies custom ref/index
#17
bede
closed
1 year ago
0
Check if input files exist
#16
bede
closed
1 year ago
0
Add aligner and index information to output json
#15
bede
closed
1 year ago
0
Avoid overwriting output unless forced
#14
bede
closed
1 year ago
0
Running multiple hostile instances on same input file(s) corrupts decontamination statistics
#13
bede
closed
8 months ago
2
Automatic masking
#12
bede
closed
1 year ago
1
Automatically choose most appropriate alignment backend for the input read type
#11
bede
closed
1 year ago
0
Crashes with exclusively contaminated input
#10
bede
closed
1 year ago
2
Adding to Bioconda
#9
rpetit3
closed
1 year ago
10
Support --custom-index
#8
bede
closed
1 year ago
1
Support for uncompressed fastq
#7
bede
closed
1 year ago
1
Support for stdin (and stdout)
#6
bede
closed
1 year ago
1
Support for unpaired short reads
#5
bede
closed
1 year ago
1
out_dir / --out-dir broken
#4
bede
closed
1 year ago
1
Return number of reads before and after decontamination
#3
bede
closed
1 year ago
1
Make fastq header stripping optional
#2
bede
closed
1 year ago
6
BAM ingest
#1
bede
closed
8 months ago
2