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SamStudio8
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reticulatus
A snakemake-based pipeline for assembling and polishing long genomes from long nanopore reads
MIT License
68
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Test sample
#56
GiangLeN
opened
2 years ago
1
Update and pin dependencies
#55
SamStudio8
opened
2 years ago
2
Kraken rule throws InputFunctionException when provided with Ilm reads
#54
tanaes
opened
3 years ago
5
Incorrect config gives unhelpful error
#53
Mulecc
opened
3 years ago
1
k2kc (ktkit count) file should be bonded with reads.cfg
#52
SamStudio8
closed
3 years ago
0
Create LICENSE
#51
SamStudio8
closed
3 years ago
0
Provide overview figure
#50
Kirk3gaard
opened
3 years ago
3
Recent changes to pre-medaka rules have forced the simg container to be required even for CPU
#49
SamStudio8
closed
4 years ago
8
Override of medaka calls_to_draft is not working
#48
jagos01
closed
4 years ago
20
Conda installation issue
#47
emmadoughty
closed
4 years ago
8
Snakemake enhancement tracking issue
#46
SamStudio8
opened
4 years ago
0
assembly stats script is well slow
#45
SamStudio8
opened
4 years ago
0
Allow enforcing of a maximum number of attempts
#44
SamStudio8
opened
4 years ago
0
Globally define wildcard_constraints
#43
SamStudio8
closed
4 years ago
0
[pomoxis] Reticulatus-pomoxis tracking issue
#42
SamStudio8
opened
4 years ago
0
Rebaled assemblies fail jts_fastmer rule
#41
SamStudio8
closed
4 years ago
5
Expected assembly size is hardcoded in the default spellbook, which isn't a very good idea
#40
SamStudio8
opened
4 years ago
1
Error when running the pipeline
#39
nbargues
closed
4 years ago
14
Ensure GPU devices are provisioned
#38
SamStudio8
closed
4 years ago
0
Add a method to mock entries in the manifest (eg. for comparison of known refs etc)
#37
SamStudio8
opened
4 years ago
0
Permit use of multiple ref.cfg, bound together by a config
#36
SamStudio8
closed
4 years ago
0
Read length statistics by reference
#35
SamStudio8
closed
4 years ago
0
Use ktkit for `extract_kraken_contigs` rule
#34
SamStudio8
opened
4 years ago
1
ktkit, download taxonomy database to config.yaml location
#33
SamStudio8
closed
4 years ago
1
Add links to ref.cfg.example to online Zymo refs
#32
SamStudio8
closed
4 years ago
0
Use of flye --meta should be configurable
#31
SamStudio8
closed
4 years ago
0
Is this for isolates or metagenomes?
#30
tseemann
closed
4 years ago
2
Assembly battery graph
#29
SamStudio8
opened
4 years ago
0
Per taxon final assembly coverage based on kraken / ktkit
#28
SamStudio8
closed
4 years ago
1
Read taxon summaries with kraken / ktkit
#27
SamStudio8
closed
4 years ago
2
Add option to manifest to trash contigs with low support (low depth)
#26
SamStudio8
opened
4 years ago
0
Add medaka `consensus_probs.hdf` to rule output and set it as temp to destroy it afterwards
#25
SamStudio8
closed
4 years ago
1
Update to new SlackLogger (when it becomes available)
#24
SamStudio8
closed
4 years ago
2
Hook subsample_bam to be usable from manifest
#23
SamStudio8
closed
4 years ago
6
Benchmark summariser can't get time spent by medaka_consensus on samtools operations
#22
SamStudio8
closed
4 years ago
2
Override ${SORT} in pomoxis mini_align to reduce medaka sort overhead
#21
SamStudio8
closed
4 years ago
5
Validate manifest
#20
SamStudio8
opened
4 years ago
1
Make use of the {attempt} key to reduce GPU requirements
#19
SamStudio8
opened
4 years ago
2
General workspace/ tidying
#18
SamStudio8
opened
4 years ago
0
General tidying
#17
SamStudio8
closed
4 years ago
1
Automatically assign log and rtbenchmark with callable
#16
SamStudio8
opened
4 years ago
1
Rename `Snakefile-full` to `Snakefile-zymo` and decouple the rules
#15
SamStudio8
closed
4 years ago
5
Using pigz to speed up gzip steps causes flye to fail
#14
SamStudio8
opened
4 years ago
3
Full benchmark mode
#13
SamStudio8
closed
4 years ago
10
Generate citations for rules
#12
SamStudio8
opened
4 years ago
1
Consider process specific reporting of GPU information
#11
SamStudio8
opened
4 years ago
1
Override snakemake benchmark timer for GPU information
#10
SamStudio8
closed
4 years ago
6
Helper commands to initialise a pipeline
#9
SamStudio8
opened
4 years ago
2
Add option to flye spell to turn off built-in polishing
#8
SamStudio8
closed
4 years ago
0
Juggle GPU medaka automatically with CUDA_VISIBLE_DEVICES
#7
SamStudio8
closed
4 years ago
1
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