5.

2: 4985 contigs
10: 4270 contigs
exp_cov auto min_contig_lgth 100:
# Run initial assembly
velveth Assem 23 -shortPaired -fastq Helya_s_r_2.fastq Holleya_s_4_1.fastq
# Get contigs
velvetg Assem -exp_cov auto -min_contig_lgth 100
# Get ORFs on Forward Strand
getorf -sequence Assem/contigs.fa -outseq Assem/orfs.fa -table 0 -minsize 300 -f
ind 3 -noreverse -sformat1 fasta -osformat2 fasta
# Get ORFs on Reverse Strand
revseq Assem/contigs.fa Assem/contigs.rev.fa
getorf -sequence Assem/contigs.rev.fa -outseq Assem/orfs.rev.fa -table 0 -minsiz
e 300 -find 3 -noreverse -sformat1 fasta -osformat2 fasta
# Convert FASTA files to NCBI formatted FASTA files
seqret Assem/orfs.fa Assem/orfs.ncbi.fa -osf ncbi
seqret Assem/orfs.rev.fa Assem/orfs.rev.ncbi.fa -osf ncbi
# Make database for forward strand and reverse stand
makeblastdb -in Assem/orfs.ncbi.fa -out Assem/dborfsfwd -parse_seqids -dbtype nu
cl
makeblastdb -in Assem/orfs.rev.ncbi.fa -out Assem/dborfsrev -parse_seqids -dbtyp
e nucl
# Blast Forward Strand and Reverse Strand to get matches
tblastx -query pbpg.fa -db Assem/dborfsfwd -strand plus > fwdmatches.txt
tblastx -query pbpg.fa -db Assem/dborfsrev -strand plus > revmatches.txt
gnl|unk|NODE_846_length_4768_cov_23.244127_1 [140 - 4465] 1337 0.
0 5
gnl|unk|NODE_553_length_2722_cov_22.938280_1 [525 - 2738] 1047 0.
0 3