Adam Voshall, Sairam Behera, Xiangjun Li, Xiao-Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon, Etsuko N. Moriyama (2021)
"A consensus-based ensemble approach to improve transcriptome assembly"
BMC Bioinformatics 22: 513
— ConSemble —
— Supplemental Information —
— A. thaliana Assemblies in Table 1 —
- Bayesembler Protein Sequences (fasta file, 16MB)
- Bayesembler Nucleotide Sequences (fasta file, 79MB)
- Cufflinks Protein Sequences (fasta file, 12MB)
- Cufflinks Nucleotide Sequences (fasta file, 59MB)
- Scallop Protein Sequences (fasta file, 19MB)
- Scallop Nucleotide Sequences (fasta file, 106MB)
- StringTie Protein Sequences (fasta file, 13MB)
- StringTie Nucleotide Sequences (fasta file, 70MB)
- IDBA-Tran Protein Sequences (fasta file, 11MB)
- IDBA-Tran Nucleotide Sequences (fasta file, 43MB)
- rnaSPAdes Protein Sequences (fasta file, 21MB)
- rnaSPAdes Nucleotide Sequences (fasta file, 86MB)
- SOAPdenovo-Trans Protein Sequences (fasta file, 11MB)
- SOAPdenovo-Trans Nucleotide Sequences (fasta file, 49MB)
- Trinity Protein Sequences (fasta file, 11MB)
- Trinity Nucleotide Sequences (fasta file, 45MB)
- EvidentialGene Protein Sequences (fasta file, 68MB)
- EvidentialGene Nucleotide Sequences (fasta file, 117MB)
- Concatenation Protein Sequences (fasta file, 22MB)
- Concatenation Nucleotide Sequences (fasta file, 91MB)
- Transborrow Protein Sequences (fasta file, 1.8MB)
- Transborrow Nucleotide Sequences (fasta file, 370KB)
- ConSemble3+d Protein Sequences (fasta file, 12MB)
- ConSemble3+d Nucleotide Sequences (fasta file, 43MB)
- ConSemble3+g Protein Sequences (fasta file, 9.0MB)
- ConSemble3+g Nucleotide Sequences (fasta file, 37MB)
— Benchmark Transcriptomes —
- no0-noAlt-reads_1.fq.bz2 (bzip file, 11GB, MD5: 2fd276ddc98b2328bf54db94d853983f)
- no0-noAlt-reads_2.fq.bz2 (bzip file, 11GB, MD5: c5027e6c495f779f301fbfa70efc839d)
- No0 Transcriptome (unique dataset) (fasta file, 8.9MB)
- col0-Alt-reads_1.fq.bz2 (bzip file, 11GB, MD5: a067b0ad8def0bdad5f2bcf4d692da78)
- col0-Alt-reads_2.fq.bz2 (bzip file, 11GB, MD5: 08d3142539456961c245abe3436f72d7)
- Col0 Transcriptome (unique dataset) (fasta file, 5.7MB)
- Human-reads_1.fq.bz2 (gzip file, 12GB, MD5: 67e586484d01fd10874219192560cebc)
- Human-reads_2.fq.bz2 (gzip file, 12GB, MD5: 7ee51324facb11321565e99e2eb1ec73)
- Human Transcriptome (unique dataset) (fasta file, 5.1MB)
— Simulation —
— (last updated: August 27, 2022) —