cdhit

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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...

ckeeling

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...

tkiryuti

-g option in cd-hit-est does not work

1

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...

marekzyw

how to run cd-hit-454 with very large file

1

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...

sekhwal

cd-hit-dup RUN error

1

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:...

sekhwal

CD-HIT ambiguous characters

1

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...

ChariteVirology

use more portable /usr/bin/env perl for scripts

6

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...

wookietreiber

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

tseemann

CD-Hit Precompiled Binaries

2

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...

samirelanduk

Segfault in 4.8.1

1

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...

epruesse