Lossless compression tool for metagenomic reads
##Requirements and Dependencies
MetaCram is suitable for all unix-like operating systems with perl installation with perl modules 1) File::Slurp 2) Array::Utils 3) Capture::Tiny.
MetaCram uses the following software packages:
- Kraken - available from https://ccb.jhu.edu/software/kraken/
- download minikraken database
- Bowtie2 - available from http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
- BLAST - available from http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
- download nt database.
- IDBA - available from http://i.cs.hku.hk/~alse/hkubrg/projects/idba/
- CRAM - 3 jar files packaged together with the script
- ExtendedGolombCRAM.jar
- GolombCRAM.jar
- HuffmanCRAM.jar
- SAMtools - available from samtools.sourceforge.net
- MFCompress - available from http://bioinformatics.ua.pt/software/mfcompress/
You will need to download and install these packages before running MetaCRAM.
MetaCram also makes use of the bacterial genome library from NCBI, which can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz. After decompressing the file, we need to combine multiple strands into one folder.
Alternatively, we recommend that you download our genus database in the specific format needed by MetaCRAM, called "genus_db_final.tgz", from https://uofi.box.com/s/sy92jv098eb0e4s277vuiod72m2jjf7c
##Commands to run MetaCRAM
Compression
perl MetaCram.pl --compress --output <output directory> --paired <path to reads> --<exGolomb, huffman, golomb>
Example:
[shared3]$ perl MetaCram.pl --compress --output /shared3/MetaCRAM_SRR359032_Huffman --paired /shared3/SRR359032_1.fasta /shared3/ SRR359032_2.fasta --huffman &>MetaCramLOG_SRR359032_Huffman.txt
Decompression
perl MetaDeCram.pl --input <path to folder containing the Round1 and Round2 folders>
Example:
[shared3]$ perl MetaDeCram.pl --input /shared3/MetaCRAM_processedSRR359032_Huffman/MetaCRAM &>decompressorLogSRR359032_Huffman.txt
(*--paired is optional)
(*<> indicates a choice)
(* to log, append “&> ”)
(Path to directories which contain various databases need to be pre-specified)
##Options
For more options, run perl MetaCram.pl --help.
##Contact Minji Kim (mkim158@illinois.edu) and Xiejia Zhang (xzhan121@illinois.edu)