Kudoa iwatai Reference Guided Transcriptome Assembly
Creators: name: Freed Ahmad
Publisher: name: figshare
Year: 2020
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Parasitology
subject: 60408 Genomics
subject: 70404 Fish Pests and Diseases
subject: FOS: Agriculture, forestry and fisheries
subject: FOS: Agriculture, forestry and fisheries
subject: 70401 Aquaculture

description: <b>Kudoa iwatai Reference Guided Transcriptome Assembly<br></b><br>This assembly is created using following commands:<br># downloaded the Kudoa iwatai genome from NCBI<br>wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/407/235/GCA_001407235.2_Kudoa1/GCA_001407235.2_Kudoa1_genomic.fna.gz<br>#unzip<br>gzip -d GCA_001407235.2_Kudoa1_genomic.fna.gz<br><br>#create HISat2 genome index<br>hisat2-build GCA_001407235.2_Kudoa1_genomic.fna KI_index<br><br>#downloaded Kudoa iwatai transcriptome reads<br>fastq-dump -I --split-files SRR1300899<br>#Read 154253215 spots for SRR1300899<br>#Written 154253215 spots for SRR1300899<br><br>#Spliced alignment on the genome<br>hisat2 -p 10 -x KI_index -q -1 SRR1300899_1.fastq -2 SRR1300899_2.fastq --dta --no-unal -S SRR1300899_ALIGN.sam<br>#154253215 reads; of these:<br># 154253215 (100.00%) were paired; of these:<br># 78924150 (51.17%) aligned concordantly 0 times<br># 46696528 (30.27%) aligned concordantly exactly 1 time<br># 28632537 (18.56%) aligned concordantly &gt;1 times<br># ----<br># 78924150 pairs aligned concordantly 0 times; of these:<br># 719952 (0.91%) aligned discordantly 1 time<br># ----<br># 78204198 pairs aligned 0 times concordantly or discordantly; of these:<br># 156408396 mates make up the pairs; of these:<br># 138764999 (88.72%) aligned 0 times<br># 10250437 (6.55%) aligned exactly 1 time<br># 7392960 (4.73%) aligned &gt;1 times<br>#55.02% overall alignment rate<br><br>samtools view -@ 4 -bS SRR1300899_ALIGN.sam -o SRR1300899_ALIGN.bam<br>samtools sort -@ 4 SRR1300899_ALIGN.bam -o SRR1300899_ALIGN_SORT.bam<br>samtools index -@ 4 SRR1300899_ALIGN_SORT.bam<br><br># assemble refernce guided transcrpitome <br>stringtie SRR1300899_ALIGN_SORT.bam -p 10 -l KI_trans -o SRR1300899_ALIGN_SORT_transcripts.gtf<br><br><br># extract the CDC sequences from the genome <br>gffread -w GCA_001407235.2_Kudoa1_genomic_StringtieCDS.fasta -g GCA_001407235.2_Kudoa1_genomic.fna SRR1300899_ALIGN_SORT_transcripts.gtf<br><br><b>References:</b><br><br><b>1. </b>Chang, ES, Neuhof, M, Rubinstein, ND, Diamant, A, Philippe, H, Huchon, D and Cartwright, P (2015) Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. Proceedings of the National Academy of Sciences of the United States of America 112, 14912–14917. doi: 10.1073/pnas.1511468112.<br><b>2.</b> Kim D., Langmead B. and Salzberg S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature methods 12, 357-360. doi: 10.1038/nmeth.3317.<br><b>3.</b> Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G. and Durbin R. (2009). The Sequence Alignment/Map format and SAMtools. Computer applications in the biosciences 25, 2078-2079. doi: 10.1093/bioinformatics/btp352.<br><b>4.</b> Pertea M., Pertea G. M., Antonescu C. M., Chang T., Mendell J. T. and Salzberg S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology 33, 290-295. doi: 10.1038/nbt.3122.