
For. H. symbiolongicarpus, twelve transcriptome assemblies were generated using Trinity, TopHat, and HISAT2/StringTie. 

Seven Trinity assemblies:

All Trinity assemblies were generated with Trinity v.2.1.1. 
Assemblies with 'allpaths' in the title indicates that reads were error corrected with the 'ErrorCorrectReads.pl' script from allpathslg-46513.
'hc12' in the title indicates that the reads were first trimmed in Trimmomatic v0.36 using "HEADCROP:12"
All genome guided assemblies 'with dta' in the title indicate that the HISAT2 alignment step included the option --dta/--downstream-transcriptome-assembly.

Trinity commands for each assembly:
Trinity_denovo_allpaths_hc12:
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_trimmomatic_hc12/HKNMYBBXX_15196318_S26_L003_1.1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_trimmomatic_hc12/HKNMYBBXX_15196318_S26_L003_1.2.fq --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_trimmomatic_hc12/trinity/

Trinity_denovo_allpaths:
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths/INTERLEAVEDREADS.ECR.FQ.paired.A.1.fastq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths/INTERLEAVEDREADS.ECR.FQ.paired.B.1.fastq --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths/trinity/

Trinity_denovo_hc12:
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/trimmomatic_hc12/HKNMYBBXX_15196318_S26_L003_1.1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/trimmomatic_hc12/HKNMYBBXX_15196318_S26_L003_1.2.fq --CPU 48 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/trimmomatic_hc12/trinity/

Trinity_allpaths_genome_guided_unmasked_with_dta:
Trinity --genome_guided_bam /data/projects/barreira/hisat2_assemblies/Hsymbio_PBJelly/out_hisat_Hsymbio_SS_RNAseq.sorted.bam --genome_guided_max_intron 10000 --SS_lib_type RF --seqType fq --max_memory 250G --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided_with_dta/trinity

Trinity_allpaths_genome_guided_unmasked_without_dta:
Trinity --genome_guided_bam /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided/out_hisat_Hsymbio_SS_RNAseq_no_dta.sorted.bam --genome_guided_max_intron 10000 --SS_lib_type RF --seqType fq --max_memory 250G --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided/trinity

Trinity_allpaths_genome_guided_masked_with_dta:
Trinity --genome_guided_bam /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided_masked_with_dta/out_hisat_maskedHsymbio_SS_RNAseq.sorted.bam --genome_guided_max_intron 10000 --SS_lib_type RF --seqType fq --max_memory 250G --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided_masked_with_dta/trinity

Trinity_allpaths_genome_guided_masked_without_dta:
Trinity --genome_guided_bam /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided_masked/out_hisat_maskedHsymbio_SS_RNAseq_no_dta.sorted.bam --genome_guided_max_intron 10000 --SS_lib_type RF --seqType fq --max_memory 250G --CPU 36 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/symbio/2017_08_15.strand_specific.170711_SONIC_HKNMYBBXX/allpaths_genome_guided_masked/trinity


One TopHat assembly (Hsym_transcriptome.fasta) was generated with TopHat v2.1.1 (command: tophat2 -p 50 -i 10 -r 72 -o ./tophat_result Hsym HKNMYBBXX_15196318_S26_L003_1.1.fq HKNMYBBXX_15196318_S26_L003_1.2.fq) against H. symbiolongicarpus unmasked assembly, 
and StringTie v1.3.4 (command stringtie accepted_hits.bam -c 1 -p 50 -m 150 -t --rf -o out_Hsymbio.gtf). Final fasta assembly file was generated with GFF utilities (command: gffread -w Hsym_transcripts.fa -g ../primary.polished.fa out_Hsymbio.gtf) 
and an in house bash script to rename the headers and the file, and restructure the sequences.

Four HISAT2/StringTie assemblies:
The HISAT2/stringtie_unmasked_genome_with_dta (HyS_hisat2_transcriptome.fasta) assembly was generated with HISAT2 v2.0.5 (command hisat2 -p 50 -q -x Hsym_pbjelly -1 HKNMYBBXX_15196318_S26_L003_1.1.fq -2 HKNMYBBXX_15196318_S26_L003_1.2.fq --rna-strandness RF --dta -S out_hisat_Hsymbio_SS_RNAseq.sam) 
against H. symbiolongicarpus unmasked assembly, SAM output converted to BAM with Samtools v1.7, and StringTie v1.3.4 (command stringtie out_hisat_Hsymbio_SS_RNAseq.sorted.bam -c 1 -p 50 -m 150 -t --rf -o out_Hsymbio_hisat.gtf). 
Final fasta assembly file was generated with GFF utilities (command: gffread -w HyS_hisat2_transcripts.fa -g primary.polished.fa out_Hsymbio_hisat.gtf) and an in house bash script rename the headers and file, and restructure the sequences.

The HISAT2/stringtie_unmasked_genome_without_dta (HyS_hisat2_transcriptome_no_dta.fasta) assembly was generated with HISAT2 v2.0.5 (command hisat2 -p 50 -q -x ../Hsym_pbjelly -1 ../HKNMYBBXX_15196318_S26_L003_1.1.fq -2 ../HKNMYBBXX_15196318_S26_L003_1.2.fq --rna-strandness RF -S out_hisat_Hsymbio_SS_RNAseq_no_dta.sam) 
against H. symbiolongicarpus unmasked assembly, SAM output converted to BAM with Samtools v1.7, and StringTie v1.3.4 (command stringtie out_hisat_Hsymbio_SS_RNAseq_no_dta.sorted.bam -c 1 -p 50 -m 150 -t --rf -o out_Hsymbio_hisat_no_dta.gtf). 
Final fasta assembly file was generated with GFF utilities (command: gffread -w HyS_hisat2_transcripts_no_dta.fa -g ../primary.polished.fa out_Hsymbio_hisat_no_dta.gtf) and an in house bash script rename the headers and the file, and restructure the sequences.

The HISAT2/stringtie_masked_genome_with_dta (maskedHyS_hisat2_transcriptome.fasta) assembly was generated with HISAT2 v2.0.5 (command hisat2 -p 50 -q -x Hsym_pbjelly_masked -1 HKNMYBBXX_15196318_S26_L003_1.1.fq -2 HKNMYBBXX_15196318_S26_L003_1.2.fq --rna-strandness RF --dta -S out_hisat_maskedHsymbio_SS_RNAseq.sam) 
against H. symbiolongicarpus masked assembly, SAM output converted to BAM with Samtools v1.7, and StringTie v1.3.4 (command stringtie out_hisat_maskedHsymbio_SS_RNAseq.sorted.bam -c 1 -p 50 -m 150 -t --rf -o out_maskedHsymbio_hisat.gtf) and an in house bash script rename the headers and the file, and restructure the sequences.

The HISAT2/stringtie_masked_genome_without_dta (maskedHyS_hisat2_transcriptome_no_dta.fasta) assembly was generated with HISAT2 v2.0.5 (command hisat2 -p 50 -q -x ../Hsym_pbjelly_masked -1 ../HKNMYBBXX_15196318_S26_L003_1.1.fq -2 ../HKNMYBBXX_15196318_S26_L003_1.2.fq --rna-strandness RF -S out_hisat_maskedHsymbio_SS_RNAseq_no_dta.sam) 
against H. symbiolongicarpus masked assembly, SAM output converted to BAM with Samtools v1.7, and StringTie v1.3.4 (command stringtie out_hisat_maskedHsymbio_SS_RNAseq_no_dta.sorted.bam -c 1 -p 50 -m 150 -t --rf -o out_maskedHsymbio_hisat_no_dta.gtf) and an in house bash script rename the headers and the file, and restructure the sequences.
********************

For H. echinata, five transcriptome assemblies were generated using Trinity.

All Trinity assemblies were generated with Trinity v2.1.1
Assemblies with 'allpaths' in the title indicates that reads were error corrected with the 'ErrorCorrectReads.pl' script from allpathslg-46513.
'hc12' in the title indicates that the reads were first trimmed in Trimmomatic v0.36 using "HEADCROP:12"

Trinity_denovo_hc12.fasta
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032602.trimmed_1.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032603.trimmed_1.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032604.trimmed_1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032602.trimmed_2.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032603.trimmed_2.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/160901_YOSHI_C92GMANXX.4.13032604.trimmed_2.fq --CPU 16 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_19.strand_specific.trimmed/trinity/

Trinity_denovo_allpaths_hc12.fasta 
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032602.trimmed_1.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032603.trimmed_1.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032604.trimmed_1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032602.trimmed_2.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032603.trimmed_2.fq,/data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/160901_YOSHI_C92GMANXX.4.13032604.trimmed_2.fq --CPU 24 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.headcrop12/trinity/

Trinity_denovo_allpaths_hc12_1strandspecific_13032602.fasta
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032602/160901_YOSHI_C92GMANXX.4.13032602.trimmed_1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032602/160901_YOSHI_C92GMANXX.4.13032602.trimmed_2.fq --CPU 24 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032602/trinity/

Trinity_denovo_allpaths_hc12_1strandspecific_13032603.fasta
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032603/160901_YOSHI_C92GMANXX.4.13032603.trimmed_1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032603/160901_YOSHI_C92GMANXX.4.13032603.trimmed_2.fq --CPU 24 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032603/trinity/

Trinity_denovo_allpaths_hc12_1strandspecific_13032604.fasta
Trinity --SS_lib_type RF --seqType fq --max_memory 250G --left /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032604/160901_YOSHI_C92GMANXX.4.13032604.trimmed_1.fq --right /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032604/160901_YOSHI_C92GMANXX.4.13032604.trimmed_2.fq --CPU 24 --output /data/projects/hydractinia/RUNNING_SOFTWARE/Trinity/echinata/2016_10_13.strand_specific.allpaths.hc12/13032604/trinity/
