maxwellshih / akutils Goto Github PK

#
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#
# This is a collection of scripts I wrote to make myself more
# productive while doing microbial ecology work with QIIME
# on a Linux system (Ubuntu 14.04).  You should be comfortable
# installing packages and such that these scripts might require.
# I will try to include in help functions what dependencies are 
# required, but here is a short list which should cover most of
# these tools:
#
# 1) QIIME 1.8.0 or later (https://qiime.org)
# 2) ea-utils (https://code.google.com/p/ea-utils/)
# 3) Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
# 4) NGSutils (http://ngsutils.org/)
# 5) Fasta-splitter.pl (http://kirill-kryukov.com/study/tools/fasta-splitter/)
# 6) ITSx (http://microbiology.se/software/itsx/)
# 7) Smalt (https://www.sanger.ac.uk/resources/software/smalt/)
# 8) HMMer v3+ (http://hmmer.janelia.org/)
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# Install these and then you can use my scripts.  Still, if
# they break for you, I probably can't help.  
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# Check out my development repository (akutils-dev) for more 
# scripts that may eventually wind up here.
#