Table 1 Performance analysis of real plant transcriptome assembly
From: A consensus-based ensemble approach to improve transcriptome assembly
Assembler | A. thaliana Col-0 (48,359)a | M. charantia (45,859)a | G. hirsutum (70,478)a | ||||||
|---|---|---|---|---|---|---|---|---|---|
# of contigsb | BUSCOc | EVALd | # of contigsb | BUSCOc | EVALd | # of contigsb | BUSCOc | EVALd | |
[Genome-guided] | |||||||||
Bayesembler | 45,583 (94) [10,611] | 1677 | − 3.18 | 44,524 (97) | 1629 | − 1.99 | NAe | NAe | NAe |
Cufflinks | 34,771 (72) [9,886] | 1593 | − 2.95 | 38,655 (84) | 1662 | − 1.64 | 98,590 (140) | 1908 | − 3.44 |
Scallop | 73,172 (151) [13,272] | 1841 | − 2.82 | 68,593 (150) | 1855 | − 1.49 | 183,625 (261) | 1967 | − 3.32 |
StringTie2 | 37,211 (77) [12,619] | 1819 | − 2.82 | 44,149 (90) | 1847 | − 1.51 | 108,389 (154) | 1998 | − 3.24 |
[De novo] | |||||||||
IDBA-Tran | 52,982 (110) [6,871] | 1287 | − 2.92 | 106,170 (232) | 657 | − 1.82 | 215,470 (306) | 411 | − 5.71 |
rnaSPAdes | 101,444 (210) [8,521] | 1475 | − 2.74 | 91,791 (200) | 1051 | − 1.50 | 211,024 (299) | 1533 | − 3.66 |
SOAPdenovo | 68,141 (141) [8,973] | 1689 | − 2.93 | 115,117 (251) | 1776 | − 1.47 | 224,718 (318) | 971 | − 6.22 |
Trinity | 50,023 (103) [7,501] | 1573 | − 2.89 | 90,347 (197) | 1779 | − 1.44 | 212,852 (302) | 1921 | − 3.60 |
[Ensemble] | |||||||||
EvidentialGene | 83,749 (173) [10,892] | 1899 | − 2.87 | 148,938 (324) | 1983 | − 1.60 | 726,828 (1,031) | 2070 | − 4.07 |
Concatenation | 70,444 (146) [12,184] | 1855 | − 2.71 | 66,613 (145) | 1923 | − 1.53 | 97,419 (138) | 2010 | − 3.76 |
ConSemble3+d | 49,713 (103) [12,659] | 1833 | − 2.73 | 90,781 (198) | 1858 | − 1.42 | 114,974 (163) | 1312 | − 5.53 |
ConSemble3+g | 24,355 (50) [11,322] | 1587 | − 1.18 | 24,699 (74) | 1718 | − 2.20 | 49,530 (54) | 1689 | − 1.13 |
TransBorrow | 1521 (3) [734] | 29 | − 2.40 | 53,191 (116) | 1896 | − 1.66 | 6234 (9) | 79 | − 2.83 |