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For 15°C assembly, a total of 31,338 assembled transcripts with average length of 403.87 bp and average coverage of 64.68 times was obtained (Table 2).
After assembly, a total of 25,253 perfect SSRs were detected within 267,199 unigenes.
After clustering and assembly, a total of 35,507 unique sequences were generated.
Within the hybrid assembly, a total of 179 SSRs were identified within 164 sequences.
After partial de novo genome assembly, a total of 139,098 perfect microsatellite loci were detected (Table 1).
After clustering and assembly, a total of 184,599 unique sequences were generated containing over 400 SSRs.
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Using a Medicago unigene set (combining the DFCI Medicago Gene Index and the PlantGDB putative transcript assemblies, a total of 87,639 sequences) as an independent metric of completeness, a total of 92.3% of the unigenes can be mapped to Mt4.0 with ≥ 90% identity and ≥ 50% coverage, which is comparable to the level in Mt3.5 [ 3].
To further improve our assembly, we aligned our supercontigs with the opossum genome assembly (Monodelphis5.0); this yielded our draft assembly with a total of 3.17 Gb assembled bases and with an N50 of 1.84 megabases (Mb) (Table 1 ).
The MIRA assembler used for the reads assembly identified a total of 31,000 possible SNPs over 4.579 Mb of sequence.
We also had access to 15,697 BAC assemblies (not all BACs had a sufficient number of reads for an assembly) for a total of about 1.80 Gbp.
Students gave $325 during the assembly and a total of $1,115 over the week, which was also donated to Mercy.
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