Lossless compression tool for metagenomic reads
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ExtendedGolombCRAM.jar
GolombCRAM.jar
HuffmanCRAM.jar
MetaCram.pl
MetaCramVMversion.pl
MetaDeCram.pl
MetaDeCramVMversion.pl
OUTsorter.pl
README.md

README.md

MetaCRAM

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:

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)