This is the release of Metagenome Standard Draft "Rifle Groundwater F2, ASSEMBLY_DATE=2018-03-21T16:05:14". IMG assembly of Rifle Groundwater F2, ASSEMBLY_DATE=2018-03-21T16:05:14 Proposal Name: Soil microbial communities from Rifle, Colorado, USA Proposal ID: 564 Analysis Project/Task ID: 1165933/215061 Sequencing Project ID(s): 1006534 Input Data: Library: CZBH Platform: Illumina HiSeq-2000 Regular (DNA) 500 bp fragment RawData: /global/dna/dm_archive/sdm/illumina/00/61/81/6181.6.39406.fastq.gz Read Pre-processing: The number of raw input reads is: 219334930 Assembly Stats: A C G T N IUPAC Other GC GC_stdev 0.2835 0.2164 0.2169 0.2832 0.0000 0.0000 0.0000 0.4333 0.1119 Main genome scaffold total: 599305 Main genome contig total: 599305 Main genome scaffold sequence total: 785242236 Main genome contig sequence total: 785242236 0.000% gap Main genome scaffold N/L50: 31781/3097 Main genome contig N/L50: 31781/3097 Main genome scaffold N/L90: 354609/415 Main genome contig N/L90: 354609/415 Max scaffold length: 1346285 Max contig length: 1346285 Number of scaffolds > 50 KB: 1180 % main genome in scaffolds > 50 KB: 17.43% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 599305 599305 785242236 785242236 100.00% 100 599305 599305 785242236 785242236 100.00% 250 597782 597782 784966007 784966007 100.00% 500 308465 308465 685596137 685596137 100.00% 1000 138479 138479 564905956 564905956 100.00% 2500 41675 41675 420055517 420055517 100.00% 5000 17428 17428 337164410 337164410 100.00% 10000 7894 7894 271925589 271925589 100.00% 25000 2844 2844 195181003 195181003 100.00% 50000 1180 1180 136895365 136895365 100.00% 100000 438 438 86054113 86054113 100.00% 250000 84 84 33497681 33497681 100.00% 500000 14 14 9929453 9929453 100.00% 1000000 2 2 2396504 2396504 100.00% Alignment of reads to final assembly: The number of reads used as input to aligner is: 219334930 The number of aligned reads is: 186131563 (85%) Assembly Methods: The assembly was produced by the JGI IMG team as part of their effort to reassemble older projects with modern assembly tools. The steps are similar to the current JGI Assembly protocol (as of 7/2017) with the notable exception of the treatment of contaminants. The JGI Assembly group filters for quality and contaminants prior to assembly, however this assembly was produced by the IMG group using the raw/unfiltered reads and contaminant contigs are treated differently. Large eukaryote contaminant contigs (human, mouse, cat, dog) are discarded but suspected prokaryote contigs are not removed and are listed in the contaminants.txt file instead. Users should be aware that microbes indicated in the contaminants file are commonly found in sequencing libraries, being introduced from the reagents used in library preparation. The raw/unfiltered reads were read corrected using bfc (r181) with kmer size of 21. The resulting reads were then assembled using SPAdes assembler (SPAdes version: 3.10.0-dev) (3) using a range of Kmers with the following options: --meta --only-assembler -k 21,33,55,77,99,127 The entire filtered read set was mapped to the final assembly and coverage information generated using bwa mem (4; version 0.7.15-r1142-dirty) using default parameters. Contaminant contigs were identified by mapping to the JGI Assembly group's standard human, dog, cat, and mouse reference databases; contigs with >= 90% length match were discarded. Putative contaminant contigs were identified by mapping contigs to JGI Assembly group's standard microbial contaminants reference database and contigs with >= 90% length match are listed in the contaminants.txt file, but not removed. If you have any questions, please contact the JGI project manager. Please indicate if your questions pertain to the IMG reassembly or the official JGI assembly. (1) B. Bushnell: BBTools software package (http://bbtools.jgi.doe.gov) (2) Li, H. BFC: correcting Illumina sequencing errors. Bioinformatics 31, 2885-2887 (2015). Doi: 10.1093/bioinformatics/btv290 (https://github.com/lh3/bfc) (3) Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P.A., 2017. metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), pp.824-834. (4) Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168] The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231