cdhit
cdhit copied to clipboard
Automatically exported from code.google.com/p/cdhit
Hello all, I have a transcriptome assembly (with no reference genome available) that appears to have some gDNA contamination such that I am seeing very similar contigs with retained introns...
Updated "psi-cd-hit-local.pl" from release V4.8.1 (from Feb 28, 2019). Line 1198: "qsub" requires a "-v" flag to pass "$j" to the qsub job Line 1200: the error message also displays...
I am running clustering of DNA sequences which are very similar and with multiple repetitions within the file. The problem is, identical sequences does not cluster together, but rather are...
I am trying cd-hit-454 to remove duplicate sequences in a file that is 850992KB of size with the following command. ---- cd-hit-454 -i /home/kumarm/CD-HIT/marge1.fasta -o /home/kumarm/CD-HIT/454_reads_95 -c 0.99 -n 10...
I am trying to RUN cd-hit-dup, however it is showing following: I downloaded the version (cd-hit-v4.8.1-2019-0228) and extracted and running the programs... command: cd-hit-dup -i /home/kumarm/CD-HIT/marge1.fasta -o /home/kumarm/CD-HIT/output.fasta ERROR: cd-hit-dup:...
Hi everyone, I have probably a simple question but didnt find any helpful answers for it yet. What does CD-HIT do with ambiguous characters in sequences? I do for example...
This is useful, e.g. if your perl is not installed in `/usr/bin` or you want to give a specific perl precendence over the one installed in `/usr/bin`. Wherever there was...
I didn't realise there was a wiki. This github README will make it much clearer where all the good information is :-) Replaces PR https://github.com/weizhongli/cdhit/pull/41
Would it be possible for precompiled binaries for the usual platforms to be provided through some means? In the same way that the NCBI provide binaries for blast+? I managed...
I'm seeing an approx 1 in 4 segfault after processing on MacOS using the 4.8.1 build 2 package. LLDB output: ``` thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS...