QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - 1) RAW DATA: LibraryName NumReads RunType ReadType FileName LIB 8406756 2x139 Illumina Std PE (cassava 1.3) AD-726-N03_pe.fastq 2) ILLUMINA STD PE READ FILTERING STATS: Reads were screened against human contaminants, synthetic oligos used in the Illumina sequencing process. Pairs of matching reads were removed from the dataset. Total input reads: 8406756 (100%) Num contam reads removed: 0 (0.0%) Artifact reads removed: 2078 (0.0%) Total reads removed: 2078 (0.0%) Total reads remaining: 8404678 (100.0%) 3) ILLUMINA STD PE READ IDENTIFICATION STATS This step identifies contaminants but does not remove them from the dataset. Total input reads: 8406756 (100%) Num contam reads identified: 2 (0.0%) - Ralstonia 2 0.00% 4) ASSEMBLY STATS: a) SPAdes with auto decontamination: Assembly stats of the SPAdes assembly with SAG contamination removed. Estimated Genome Recovery using Single-copy Gene Analysis: archaea HMM: 85.27% bacteria HMM: 80% Largest Contig: 38.1 KB A C G T N IUPAC Other GC GC_stdev 0.3278 0.1723 0.1620 0.3380 0.0000 0.0000 0.0000 0.3342 0.0104 Main genome scaffold total: 16 Main genome contig total: 16 Main genome scaffold sequence total: 0.329 MB Main genome contig sequence total: 0.329 MB 0.000% gap Main genome scaffold N/L50: 6/21.652 KB Main genome contig N/L50: 6/21.652 KB Max scaffold length: 38.07 KB Max contig length: 38.07 KB Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.00% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 16 16 328,715 328,715 100.00% 10 KB 16 16 328,715 328,715 100.00% 25 KB 4 4 120,917 120,917 100.00% b) SPAdes assembly: Assembly stats of the SPAdes assembly. Estimated Genome Recovery using Single-copy Gene Analysis: archaea HMM: 87.86% bacteria HMM: 82.96% Largest Contig: 38.1 KB A C G T N IUPAC Other GC GC_stdev 0.3278 0.1717 0.1644 0.3362 0.0000 0.0000 0.0000 0.3360 0.0211 Main genome scaffold total: 63 Main genome contig total: 63 Main genome scaffold sequence total: 0.523 MB Main genome contig sequence total: 0.523 MB 0.000% gap Main genome scaffold N/L50: 11/18.447 KB Main genome contig N/L50: 11/18.447 KB Max scaffold length: 38.07 KB Max contig length: 38.07 KB Number of scaffolds > 50 KB: 0 % main genome in scaffolds > 50 KB: 0.00% Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 63 63 522,925 522,925 100.00% 1 KB 63 63 522,925 522,925 100.00% 2.5 KB 48 48 490,761 490,761 100.00% 5 KB 29 29 423,733 423,733 100.00% 10 KB 17 17 339,344 339,344 100.00% 25 KB 4 4 120,917 120,917 100.00% 5) NCBI SCREENING STATS This step identifies potential contaminants screened by NCBI for submission. ** No potential contaminants found. 6) KEY PIPELINE CMDS: a) Contamination removal step: Bwa version: 0.6.2-r126 Bwa aln params: Bwa sampe params: -A -P -s b) Artifact removal step: duk params: -k 22 -s 1 -c 1 c) SPAdes assembly step: SPAdes version: 3.5.0 SPAdes params: -t 8 -m 40 --sc --careful --12 7) WORKFLOW STEPS: 1. Removed contamination (human contaminants). 2. Removed illumina artifacts (synthetic oligos used in the laboratory). 3. Created SPAdes assembly of the contam+artifact filtered data. 4. Performed automated SAG decontamination on the SPAdes assembly. 8) ASSEMBLERS USED: SPAdes (v.3.5.0) 9) ASSESSED GENOME PROJECT STANDARD: Standard Draft 10) RELEASE DATE: 07/02/2015 11) AUTHORS: For additional information, please contact: NAME_OF_ANALYST - ANALYST@lbl.gov Stephan Trong - strong@lbl.gov Alex Copeland - accopeland@lbl.gov This file was automatically generated by the jigsaw pipeline software (version 2.5.1).