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===Single-end data analysis=== *Whole reads alignment using Bowtie => genome coverage calculate **Script: Read2coverage-kz-3 **Data resource: HC-MDA-Ecoli-SAGs-Ind1to8 (SE reads data set) **Template:E.coli-k12-mg1655 template **Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals **Downstream: Data was used for genome coverage calculation. [[File:sam120610-wholereadbotie-2.jpg|800px]] *Using the same alignment processing, I extract the failed-to-aligned and non-specific reads into different folder. **Script: Read2coverage-kz4 **Data resource: HC-MDA-Ecoli-SAGs-Ind1to8 **Template:E.coli-k12-mg1655 template **Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals --un [failed-to-aligned file output] --max [nonspecific file output] *ABySS de novo assembly of failed-to-align reads with (using single-end assembly with k-mer 27) **Using abyss-fac function to calculate statistics '''ABySS-fac report''' [[File:sam120610-abyss assembly of fail-to-aligne reads.jpg|700px]] *Length filtering and keep only >300bp contigs. **Script: seqLenFilger.pl *Perform BLAST on filtered contigs **BLAST setting: -K 1 -m 8 -a 2 -v 1 βb 1(using -m 8 output format to extract GI number) **BLAST setting: -K 1 -m 8 -a 2 -v 1 βb 1(using -m 9 output format to get BLAST statistics) ***'''NOTE''': Use -K 1 -v 1 -b 1 for reporting only one hit **Taxonomic analysis by NCBI Batch Entrez (against nucletide database). Transform GI number to UID for taxonomic analysis
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