anV: Raw Reads QC

k-mers are substrings of length k. Example
Why k-mers are required

De Bruijn graph a directed graph representing overlaps between sequences of symbols
Example

A Quality Control Tool. Works on FASTQ, SAM and BAM files

Navigate to bgap directory and activate qc

$ cd Desktop/bgap
            $ conda deactivate
            $ conda activate qc

Open FastQC GUI. Analyze and save the reports
```
$ fastqc
```
See the Basic statistics, Per base quality, Sequence length distribution, Overrepresented sequences and Adapter content sections

Run bbduk. Copied adapters file

$ mkdir bb_out
            $ cd bb_out
            $ bbduk.sh in1=../reads/a45_R1.fastq in2=../reads/a45_R2.fastq out1=a45_R1.fastq out2=a45_R2.fastq ref=adapters.fa k=23 mink=7 ktrim=r hdist=1 qtrim=r trimq=20 minlen=100 tpe tbo

Explanation:

Result

            Input:                  	1741880 reads 		436749684 bases.
            QTrimmed:               	1522186 reads (87.39%) 	103642774 bases (23.73%)
            KTrimmed:               	376743 reads (21.63%) 	13100754 bases (3.00%)
            Trimmed by overlap:     	8692 reads (0.50%) 	88862 bases (0.02%)
            Total Removed:          	170588 reads (9.79%) 	116832390 bases (26.75%)
            Result:                 	1571292 reads (90.21%) 	319917294 bases (73.25%)

Open FastQC GUI. Analyze and save the reports
```
$ fastqc
```

Run trimmomatic. Using BBDuk adapters file

$ mkdir trim_out
            $ cd trim_out
            $ trimmomatic PE -phred33 ../reads/a45_R1.fastq ../reads/a45_R2.fastq a45_R1_paired.fq.gz a45_R1_unpaired.fq.gz a45_R2_paired.fq.gz a45_R2_unpaired.fq.gz ILLUMINACLIP:../adapters.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:100

Input Read Pairs: 870940 Both Surviving: 599798 (68.87%) Forward Only Surviving: 160897 (18.47%) Reverse Only Surviving: 28249 (3.24%) Dropped: 81996 (9.41%)
Open FastQC GUI. Analyze and save the reports
```
$ fastqc
```

Raw Reads QC

(Bacterial Genome Analysis Piplene)