snayfach IGGsearch issues

snayfach / IGGsearch

Metagenomic species profiling with enhanced coverage of the human gut microbiome

GNU General Public License v3.0

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issues

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Default value for min_sp_quality

#32 jannemm closed 4 months ago
1
Bug in merge?

#31 Javelarb closed 5 years ago
3
Make possible to install using pip or conda

#30 boulund opened 5 years ago
2
custom database

#29 alienzj closed 5 years ago
1
is it SAM/BAM format? Consider opening with check_sq=False

#28 nbutyrate closed 5 years ago
4
Comparison to MIDAS

#27 durrantmm opened 5 years ago
1
customized database of species-specific marker genes

#26 yejunbin closed 5 years ago
1
minor tweak so it runs under python3

#25 boris-dimitrov closed 1 year ago
1
remove old files

#24 snayfach closed 5 years ago
0
add .gitignore

#23 snayfach closed 5 years ago
0
allow user to supply list of markers or species to exclude

#22 snayfach closed 5 years ago
1
add license

#21 snayfach closed 5 years ago
0
Peak RAM

#20 snayfach closed 5 years ago
0
check for existence of input files

#19 snayfach closed 5 years ago
0
RuntimeWarning: Mean of empty slice.

#18 snayfach closed 5 years ago
0
Add support for FASTA

#17 snayfach closed 5 years ago
1
Update README

#16 snayfach closed 5 years ago
0
Evaluate USCMGs

#15 snayfach closed 5 years ago
0
Option to report all species or only detected species

#14 snayfach closed 5 years ago
1
Add presence/absence information to output file

#13 snayfach closed 5 years ago
0
Report total # of % of reads mapped, # of species detected

#12 snayfach closed 5 years ago
0
Add option to exclude species based on genome-quality

#11 snayfach closed 5 years ago
0
Provide full database and gut-only database

#10 snayfach closed 5 years ago
0
Support for bowtie2

#9 snayfach closed 5 years ago
0
Support for BIOM format

#8 snayfach closed 5 years ago
0
Add taxonomy information

#7 snayfach closed 5 years ago
0
Paired end reads

#6 snayfach closed 5 years ago
0
Species names

#5 snayfach closed 5 years ago
0
—mapid (works; may use narrower value range, e.g. 50 and 1 have same results)

#4 zjshi closed 5 years ago
0
—min_intra_freq (using 0.1, 0.5, 0.9 yielded same results)

#3 zjshi closed 5 years ago
0
Add description and default values in help text for -w, —min_intra_freq and --max_inter_freq flag

#2 zjshi closed 5 years ago
0
Add taxonomic info to the output

#1 zjshi closed 5 years ago
1