deep_seq_analysis

The project uses reference based alignment as well as de novo assembly and summarizes the results from WGS analysis of a dataset obtained from SRA database. The experimental design involved trimming the sequence using BRAT [http://compbio.cs.ucr.edu/brat/BRAT_USER_MANUAL_1_2_3.pdf]. Reference based alignment was done using bowtie [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml] and the output files were indexed using Samtools[http://www.htslib.org/doc/samtools.html]. The De novo assembly was assesed using Velvet. Both the assemblies were assessed by contig N50/N90 values, percentage coverage and average depth. The reference based assembly was also used to find out the number of SNPs/Indels.