Command table

Command	Description
cat /P/y16/term3/block3/adapters/*.fa >> adapters.fasta	File with adaptors
java -jar /nfs/srv/databases/ngs/suvorova/trimmomatic/trimmomatic-0.30.jar SE -phred33 SRR4240379.fastq SRR.fastq ILLUMINACLIP:adapters.fasta:2:7:7 java -jar /nfs/srv/databases/ngs/suvorova/trimmomatic/trimmomatic-0.30.jar SE -phred33 SRR.fastq SRRtrimm.fastq TRAILING:20 MINLEN:30	Adapters deletion and sequence trimming After adapters deletion: Input Reads: 7400155 Surviving: 7269845 (98,24%) Dropped: 130310 (1,76%) After trimming: Input Reads: 7269845 Surviving: 6993284 (96,20%) Dropped: 276561 (3,80%)
velveth ./velvet 29 -short -fastq SRRtrimm.fastq	Velveth helps you construct the dataset for the following program, velvetg, and indicate to the system what each sequence file represents. 29 is the lendth of k-mers
velvetg ./	Velvetg is the core of Velvet where the de Bruijn graph is built then manipulated. Results: n50 of 31053, max 82103

Command table

Contig analysis

ID	Length (k-mers)	E-value	% Identity	Gaps / %	Chains	Chr coordinates	Part chr length	Read coordinates	Part read length	Coverage
5	82103	0.0/td>	77%	2%/td>	+/+	451729 - 529004	77276	2388 - 82131	79744	47.938393
2	70497	0.0	81	2%	+/+	528977 - 594099	65423	1-67134	67134	49.610836
6	49941	0.0	75	4%	+/+	49941 - 173180	123240	53 - 45435	45383	48.604492

Contig №5

The longest contig №5, as it can be seen, there are 14 different alingments:

            1. 451729 - 454069
            2. 462496 - 467421
            3. 467412 - 474667
            4. 474844 - 480660
            5. 480874 - 481545
            6. 481997 - 488106
            And 8 more...

Chromosome coordinates It is also clearly seen that coordinates and the length of these alignments match with what is observed on dot-matrix view.

Contig №2

Number of Matches: 8. The gap between the last two alignments is big and therefore it can be presumed that this contig is not as similar to the original sequence as desired.

Contig №6

Number of Matches: 5.

            1. 127825 - 140555
            2. 144368 - 151796
            3. 153752 - 161738
            4. 161898 - 166752
            5. 166750 - 173180

And once again it is seen that coordinates and length fit with the image. Although, it can be seen that the last alingment is a theoretical continuation of the previous one, however the coordinats of contig are different: 38961 (the end of alignment 4 and 38992 - the beggining of alignment 5) therefore it is 2 different alignments.

All in all, it is can be concluded that the final assemly is acceptable.