git clone https://github.com/jameslz/atlas-utils
cd atlas-utils
makecurrent: version：0.0.2
Usage: atlas-utils <command> <arguments>
Version: 0.0.2
Command:
-- Fastq manipulation.
demultiplex FASTAQ demultiplex with barcode sequence.
uniques find unique sequences and abundances.
linkpairs link paired-reads with padding 'N'.
fqchk fastq QC (base/quality summary).
label add label to fasta headline.
barcode get barcode seq from paired-reads.
orient orient seq use strand +/- information.
maxee qualtiy control with quality error.
primer_strip retrive sequence region matches to primer pair.
support single end match.
-- (Z)OTU manipulation.
unique_table construct uniques table using exact match.
annotation annotate OTU table using OTU assignment from Sintax/RDP.
filter 1. Filter sequence from Mitochondria/Chloroplast, 2. optional filter
specifed taxon level .
level abundance table for specify taxonomy level. ie. genus.
abundance abundance table for specify taxonomy level and sample. ie. genus.
summary calcuate OTU number/Tag number per sample.
rowsum calcuate row sum.
rank rank/merge for numeric table.
krona convert annotated OTU table to krona text format.
quantile calcuate nth quantile sample size for otu_table normalization.
mean_size calcuate 'Mean' sample size for otu_table normalization.
min_size calcuate 'Min' sample size for otu_table normalization.
max_size calcuate 'Max' sample size for otu_table normalization.
counts2freqs convert counts table from counts to frequencies.
trim delete low-abundance (Z)OTUs with sum threshold.
prune delete low-abundance (Z)OTUs.with per sample threshold
binary convert (Z)OTUs table to presence/absence values.
pairwise convert (Z)OTUs table to pairwise format for phylocom.
rarity rarity summary.
rare rarefy OTU table to specified number of reads.
core core microbiome per/group.
group_by group_by operation for OTU table, support average, sum.
flatten flatten the zotu table taxonomy annotation.
unpack unpack the sintax classify result.
lefse convert to lefse compatibility format.
subgroup retrieve columns in in list of columns.
hierarchy hierarchy format for classic annotated OTU table.
cv calcuate C.V|Coefficient of Variation.
fish select OTUs using specifed abundance threshold.
stack reshape OTU table for data visulization.
-- PICRUSt.
normalization normalize OTU table with 16S copy Number, et..
aggregate merge same hits with sum opt.
contrib calculate feature abundance contribution.
melt calculate feature abundance. ie. KEGG, COG, with Greengene 13.5.
kann calculate feature abundance using feature maps, KO -> Module.
-- auxiliary utils.
view view text file, ignor comments and blank lines.
getline get target line with headline.
subsamples get target columns with headline match.
partition split OTU table into specify number file.
dt2xlsx convert data table (multi-) file to Excel file..
strip strip any char from first space in first columns.
Licenced:
(c) 2019-2022 - LEI ZHANG
Logic Informatics Co.,Ltd.
zhanglei@logicinformatics.com