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Freevini
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Metagenomics_pipeline
Metagenomic analysis pipeline for the BMC Microbiology paper 2019
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Confirm that use of BLAST's `-max_target_seqs` is intentional
#47
armish
opened
6 years ago
0
polish pacbio assembly
#46
Freevini
opened
6 years ago
0
Assemble Illumina reads
#45
Freevini
opened
6 years ago
0
check the rawReads file
#44
Freevini
closed
6 years ago
1
nucmer of final analysis
#43
Freevini
opened
6 years ago
0
check if circlator
#42
Freevini
closed
6 years ago
0
minimap2 unmapped against eachother
#41
Freevini
opened
6 years ago
0
subset Lapraz reads
#40
Freevini
opened
6 years ago
2
try out long read specific Metagenome tools
#39
Freevini
opened
6 years ago
1
MEGAN long read pipeline
#38
Freevini
opened
6 years ago
1
smrtlink commandline
#37
Freevini
closed
6 years ago
1
usage of smrtlinkr
#36
Freevini
closed
6 years ago
1
crispr target calling on phage
#35
Freevini
opened
6 years ago
0
Kaiju implementation
#34
Freevini
closed
6 years ago
3
second arrow polishing
#33
Freevini
closed
6 years ago
1
incorporate Quast/metaquast to compare genome assemblies
#32
Freevini
closed
6 years ago
1
sortmeRNA
#31
Freevini
opened
6 years ago
0
check Cottens assembly
#30
Freevini
closed
6 years ago
1
polish with freebase
#29
Freevini
closed
6 years ago
1
compute GC
#28
Freevini
closed
6 years ago
1
MG-rast
#27
Freevini
opened
6 years ago
0
OTU clustering
#26
Freevini
opened
6 years ago
1
Prokka implementation
#25
Freevini
closed
6 years ago
1
PanPhlAn
#24
Freevini
opened
6 years ago
0
arrow polishing
#23
Freevini
closed
6 years ago
1
mauve mapping
#22
Freevini
closed
6 years ago
1
blobology rerun
#21
Freevini
closed
6 years ago
1
implement PHASTER
#20
Freevini
opened
6 years ago
0
MVP implementation
#19
Freevini
opened
6 years ago
0
flye assembly of unmapped (plasmid-assembly)
#18
Freevini
closed
6 years ago
1
implement nucmer
#17
Freevini
closed
6 years ago
1
ngmlr/sniffles
#16
Freevini
closed
6 years ago
1
implement phaster
#15
Freevini
closed
6 years ago
1
create a timestamp
#14
Freevini
closed
6 years ago
1
blast all raw reads
#13
Freevini
closed
6 years ago
1
correct raw read mapping
#12
Freevini
closed
6 years ago
1
estimate coverage and metagenome
#11
Freevini
closed
6 years ago
1
check assemblies
#10
Freevini
closed
6 years ago
1
multifastqc of rawdata
#9
Freevini
closed
6 years ago
1
fastqc for all raw reads
#8
Freevini
closed
6 years ago
1
plasmid assembly also for lapraz
#7
Freevini
closed
6 years ago
1
no metaphlan output for cottens
#6
Freevini
closed
6 years ago
1
reduce word size in blastn
#5
Freevini
closed
6 years ago
2
add Humann2 functional annotation
#4
Freevini
closed
6 years ago
1
add mOTU
#3
Freevini
closed
6 years ago
1
shortcut location
#2
Freevini
closed
6 years ago
1
file locations
#1
Freevini
closed
6 years ago
1