Classifier for metagenomic sequences
C++ Python Objective-C Perl C Makefile Shell
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
centrifuge.xcodeproj fixed the wrong names: hisat to centrifuge Nov 4, 2016
doc Correct centrifuge-download call in manual (fixes #55) Apr 3, 2018
evaluation . Aug 16, 2016
example Update the index in example. May 19, 2018
indices Switch ls | grep to find Jun 1, 2017
third_party Added HyperLogLog++ counter and MurmurHash Apr 27, 2015
.gitignore Added a small example for Centrifuge Jan 27, 2016
AUTHORS No commit message Feb 10, 2015
LICENSE No commit message Feb 10, 2015
MANUAL Correct centrifuge-download call in manual (fixes #55) Apr 3, 2018
MANUAL.markdown Correct centrifuge-download call in manual (fixes #55) Apr 3, 2018
Makefile Add C++11 compile flags Jun 7, 2018
NEWS Updated NEWS, changed output format a bit, and add some missing files… May 25, 2016
README.md Update index names, fixes #45 Dec 6, 2016
TUTORIAL No commit message Feb 10, 2015
VERSION Update version to 1.0.4 Apr 19, 2018
aligner_bt.cpp No commit message Mar 18, 2015
aligner_bt.h No commit message Mar 18, 2015
aligner_cache.cpp No commit message Mar 18, 2015
aligner_cache.h No commit message Mar 18, 2015
aligner_metrics.h No commit message Feb 10, 2015
aligner_result.h Implemented traversing up the taxonomy tree when many assignments wer… Feb 8, 2016
aligner_seed.cpp No commit message Mar 18, 2015
aligner_seed.h No commit message Mar 18, 2015
aligner_seed_policy.cpp No commit message Feb 10, 2015
aligner_seed_policy.h No commit message Feb 10, 2015
aligner_sw.cpp No commit message Mar 18, 2015
aligner_sw.h No commit message Mar 18, 2015
aligner_sw_common.h No commit message Mar 18, 2015
aligner_sw_nuc.h No commit message Mar 18, 2015
aligner_swsse.cpp No commit message Mar 18, 2015
aligner_swsse.h No commit message Mar 18, 2015
aligner_swsse_ee_i16.cpp Removed compile warnings in Xcode 7.2 Dec 15, 2015
aligner_swsse_ee_u8.cpp Removed compile warnings in Xcode 7.2 Dec 15, 2015
aligner_swsse_loc_i16.cpp Removed compile warnings in Xcode 7.2 Dec 15, 2015
aligner_swsse_loc_u8.cpp Removed compile warnings in Xcode 7.2 Dec 15, 2015
aln_sink.h Fix unsigned comparison compiler warnings Apr 19, 2018
alphabet.cpp No commit message Feb 10, 2015
alphabet.h No commit message Feb 10, 2015
assert_helpers.h added macro to avoid 'variable unset' warnings in production build May 18, 2015
binary_sa_search.h No commit message Feb 10, 2015
bitpack.h No commit message Feb 10, 2015
blockwise_sa.h Parallelized V-Sorting Dec 18, 2015
bt2_idx.cpp Implemented --host-taxids and --exclude-taxids, and implemented a fas… Feb 11, 2016
bt2_idx.h Fix unsigned comparison compiler warnings Apr 19, 2018
bt2_io.h Change some error msg Apr 15, 2018
bt2_util.h No commit message Feb 10, 2015
btypes.h No commit message Feb 10, 2015
ccnt_lut.cpp No commit message Feb 10, 2015
centrifuge Only use one child process at a time. May 14, 2018
centrifuge-BuildSharedSequence.pl It seems --coords option is not supported in Nucmer now, so use show-… Apr 11, 2018
centrifuge-RemoveEmptySequence.pl Added executable permissions to perl scripts Nov 4, 2016
centrifuge-RemoveN.pl Added executable permissions to perl scripts Nov 4, 2016
centrifuge-build . Jan 27, 2016
centrifuge-compress.pl Check nucmer and jellyfish in centrifuge-compress Nov 10, 2016
centrifuge-download Try 2 more times before throwing the downloading error Apr 15, 2018
centrifuge-inspect Changed Manual and centrifuge-inspect script Jan 27, 2016
centrifuge-kreport Check whether a tax id is in the tree or not. Jun 8, 2018
centrifuge-promote Fix a typo Nov 29, 2017
centrifuge-sort-nt.pl Fixed bug in centrifuge-sort-nt.pl Sep 26, 2016
centrifuge.cpp Add -k option to the help message. Jun 5, 2018
centrifuge_build.cpp Remove the --large-index option from build and inspect usage. Apr 9, 2018
centrifuge_build_main.cpp No commit message Mar 12, 2015
centrifuge_compress.cpp change to unsigned Apr 23, 2015
centrifuge_inspect.cpp Remove the --large-index option from build and inspect usage. Apr 9, 2018
centrifuge_main.cpp No commit message Feb 11, 2015
centrifuge_report.cpp Added centrifuge-report for species level reporting Apr 23, 2015
classifier.h Fix unsigned comparison compiler warnings Apr 19, 2018
diff_sample.cpp No commit message Feb 10, 2015
diff_sample.h Fix misleading indentation warnings Apr 19, 2018
dp_framer.cpp No commit message Mar 18, 2015
dp_framer.h No commit message Mar 18, 2015
ds.cpp No commit message Feb 10, 2015
ds.h Fix bug introduced by commit 42b7845 Apr 4, 2018
edit.cpp No commit message Feb 10, 2015
edit.h No commit message Feb 10, 2015
endian_swap.h Removed compile warnings in Xcode 7.2 Dec 15, 2015
fast_mutex.h Removed executable permission from source files Nov 4, 2016
filebuf.h No commit message Feb 10, 2015
formats.h No commit message Feb 10, 2015
functions.sh Move the scripts path Feb 8, 2016
group_walk.cpp No commit message Feb 10, 2015
group_walk.h Removed compile warnings in Xcode 7.2 Dec 15, 2015
hi_aligner.h . Feb 5, 2016
hier_idx.h Incoporated a conversion table into the index Dec 13, 2015
hier_idx_common.h No commit message Feb 10, 2015
hyperloglogbias.h Added HyperLogLog++ counter and MurmurHash Apr 27, 2015
hyperloglogplus.h fixed HLL algorithm Feb 25, 2016
limit.cpp No commit message Feb 10, 2015
limit.h No commit message Feb 10, 2015
ls.cpp No commit message Feb 10, 2015
ls.h No commit message Feb 10, 2015
mask.cpp No commit message Feb 10, 2015
mask.h No commit message Feb 10, 2015
mem_ids.h No commit message Feb 10, 2015
mm.h No commit message Feb 10, 2015
multikey_qsort.h Switched a recursive function, mkeyQSortSuf2, to use iteration Dec 18, 2015
opts.h Add the option separator to print a separator in the classification o… Mar 26, 2018
outq.cpp No commit message Feb 10, 2015
outq.h No commit message Feb 10, 2015
pat.cpp Implemented direct access to SRA data Mar 8, 2016
pat.h Implemented direct access to SRA data Mar 8, 2016
pe.cpp No commit message Feb 10, 2015
pe.h No commit message Feb 10, 2015
presets.cpp No commit message Feb 10, 2015
presets.h No commit message Feb 10, 2015
processor_support.h No commit message Feb 10, 2015
qual.cpp No commit message Feb 10, 2015
qual.h No commit message Feb 10, 2015
random_source.cpp No commit message Feb 10, 2015
random_source.h No commit message Feb 10, 2015
random_util.cpp No commit message Feb 10, 2015
random_util.h No commit message Feb 10, 2015
read.h No commit message Feb 10, 2015
read_qseq.cpp No commit message Feb 10, 2015
ref_coord.cpp No commit message Feb 10, 2015
ref_coord.h Added documentation Mar 5, 2015
ref_read.cpp Warn one time of N empty reference sequences instead of N times Sep 26, 2016
ref_read.h Change some error msg Apr 15, 2018
reference.cpp added macro to avoid 'variable unset' warnings in production build May 18, 2015
reference.h No commit message Feb 10, 2015
scoring.cpp No commit message Feb 10, 2015
scoring.h No commit message Mar 18, 2015
search_globals.h No commit message Feb 10, 2015
sequence_io.h No commit message Feb 10, 2015
shmem.cpp No commit message Feb 10, 2015
shmem.h No commit message Feb 10, 2015
simple_func.cpp No commit message Feb 10, 2015
simple_func.h No commit message Feb 10, 2015
sse_util.cpp No commit message Mar 18, 2015
sse_util.h No commit message Mar 18, 2015
sstring.cpp No commit message Feb 10, 2015
sstring.h Fixed k-mer counting in centrifuge inspect Feb 25, 2016
str_util.h No commit message Feb 10, 2015
taxonomy.h Additional fix for -k option Sep 8, 2016
threading.h No commit message Feb 10, 2015
timer.h No commit message Feb 10, 2015
tinythread.cpp Removed executable permission from source files Nov 4, 2016
tinythread.h Removed executable permission from source files Nov 4, 2016
tokenize.h No commit message Feb 10, 2015
util.h Added species taxonomy ID column Feb 11, 2016
word_io.h Removed compile warnings in Xcode 7.2 Dec 15, 2015
zbox.h No commit message Feb 10, 2015

README.md

Centrifuge

Classifier for metagenomic sequences

[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers

The Centrifuge hompage is http://www.ccb.jhu.edu/software/centrifuge

The Centrifuge preprint is available at http://biorxiv.org/content/early/2016/05/25/054965.abstract

The Centrifuge poster is available at http://www.ccb.jhu.edu/people/infphilo/data/Centrifuge-poster.pdf

For more details on installing and running Centrifuge, look at MANUAL

Quick guide

Installation from source

git clone https://github.com/infphilo/centrifuge
cd centrifuge
make
sudo make install prefix=/usr/local

Building indexes

We provide several indexes on the Centrifuge homepage at http://www.ccb.jhu.edu/software/centrifuge. Centrifuge needs sequence and taxonomy files, as well as sequence ID to taxonomy ID mapping. See the MANUAL files for details. We provide a Makefile that simplifies the building of several standard and custom indices

cd indices
make p+h+v                   # bacterial, human, and viral genomes [~12G]
make p_compressed            # bacterial genomes compressed at the species level [~4.2G]
make p_compressed+h+v        # combination of the two above [~8G]