https://github.com/seqan/slimm
Species Level Identification of Microbes from Metagenomes
https://github.com/seqan/slimm
Last synced: about 1 year ago
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Species Level Identification of Microbes from Metagenomes
- Host: GitHub
- URL: https://github.com/seqan/slimm
- Owner: seqan
- License: other
- Created: 2016-02-04T15:45:01.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2019-04-30T11:37:11.000Z (about 7 years ago)
- Last Synced: 2025-03-23T23:26:58.936Z (over 1 year ago)
- Language: C++
- Size: 32.5 MB
- Stars: 28
- Watchers: 5
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
SLIMM - Species Level Identification of Microbes from Metagenomes
=================================================================
a taxonomic profiling tool that investigates which microorganisms are present in a sequenced sample. SLIMM requires a BAM/SAM alignment file as an input. One can use a read mapper of choice to map raw reads obtained from a sequencing machine to obtain the BAM/SAM file required as input for SLIMM.
slimm_build [OPTIONS] -nm names.dmp -nd nodes.dmp FASTA_DB nucl_gb.accession2taxid
slimm [OPTIONS] $SLIMM_DB_PATH $SAM_FILE_PATH
Try 'slimm --help' for more information.
VERSION
* SLIMM version: 0.3.0
* Last update: February 2018
### Downloads:
#### Executables
Pre-built executables for Linux and Mac are made available at the [releases page]( https://github.com/seqan/slimm/releases/latest).
#### Source code
You can build SLIMM from its source. Instruction on how to build from source can be found at the [slimm wiki] (https://github.com/seqan/slimm/wiki)
#### Cite us
If you use SLIMM in your work-flows, don't forget to cite us.
Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138 https://doi.org/10.7717/peerj.3138