New Assembler named as Bridger which combined the features from exist assemblers, i.e. Cufflinks (Reference based assembler)and trinity (denovo assembler) to overcome/improve the multiple k mer statergy which used in earlier de-novo assemblers for assemble the low and highly expressed transcripts and to get the realible Isoforms.
Bridger is available at https://sourceforge.net/projects/rnaseqassembly/files/?source=navbar webcite.
Example Command #
Bridger.pl --seqType fq --left Pair_R2.fq --right Pair_R1.fq --kmer_length 25 --CPU 30 --output k25 --clean
- From my expereince its performed well in lottia transcriptome assembly, when compared to Trinity, Trans ABySS and Oases. The quantitative metircs are CEGMA and % of reference mapping.
output files #
At present its not able to assemble combination of (Pair and Single)