search

soedinglab / plass

sensitive and precise assembly of short sequencing reads
https://plass.mmseqs.com
GNU General Public License v3.0
145 stars 13 forks source link

Combining single and paired reads #8

Closed mooreryan closed 5 years ago

mooreryan commented 5 years ago

Just wondering, is there any way to combine single and paired reads from the same library into a single assembly?

martin-steinegger commented 5 years ago

There is no internal solution to use paired end reads and single end at the same time. But you could used FLASH (https://ccb.jhu.edu/software/FLASH/) to merge the reads and concat them with the single end reads and just use a single parameter. 

     plass assemble reads.fastq assembly.fasta tmp
mooreryan commented 5 years ago

Perfect, that's exactly what I tried to do!