halc
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lanl001
High Throughput Algorithm for Long Read Error Correction
Hello, I am trying to HALC to error correct long reads using contigs generated from short reads (using rnaSpades). I have converted the multiline fasta output of rnaSpades to single...
I am trying to use HALC to correct long reads. I get this output that I haven't figured out how to use: [e.sierra@login3 output]$ head HALC.corrected.fa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
HALC fails at BLASR step. The installed BLASR version is 3.5.2. Here is the output log: > > WARNING: ./temp/step2 was found. Automatically started from step2 > 2018-09-28 17:14:37.901244 >...
There are three output.fa Error corrected full long reads. HALC.corrected.fa Error corrected trimmed long reads. HALC.split.fa Error corrected split long reads. HALC.trim.fa which could be used in downstream analysis？
Hi guys, I've been trying to use Halc for hybrid error correction of PacBio reads. The program has split my raw PB reads into 80 chunks and has successfully finished...
Hello, The pipeline keeps failing at step 4. This step seems to complete and produces output but then fails with several HDF5 errors. Here is an excerpt of the ./temp/step4/LoRDEC.err...
Hi im a newbie with installing software like this. I type make all and get this message. I try to run runHALC.py and it says "command not found". Please need...
