cdhit

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Does it mean the longest contig from a cluster is kept (if the input is an assembly)?

Rob-murphys

CD-HIT para for SLURM

3

I'd like to run the cd-hit-para.pl script on a SLURM cluster? Is this possible? Is there any way to manually split up the task to be distributed over a large...

snayfach

cd-hit-para.pl issue

4

Hi, I am processing quite a big sequencing file (40~50M reads fastq) and tried it using cd-hit-para.pl script to incorporate mpi option for it. Somehow it was running for almost...

leebo0731

Hi, I am running CD-HIT for very large files. Warning: Some seqs are too long, please rebuild the program with make parameter MAX_SEQ=new-maximum-length (e.g. make MAX_SEQ=10000000) Not fatal, but may...

Ahmedbargheet

cd-hit-est estimated consume time

1

Hi, I'm using cd-hit-est to cluster my contigs file, There is 3364268 contigs in a file(8.1G), I run it with 15 CPUs with memory 20G, It's been running for 15...

zhou-sumei

When I am using cd-hit-est and put it into the server background like this `nohup cd-hit-est -i ./trinity_out_assembly/Trinity.fasta -o ./2.cd-hit/Trinity90.fasta -c 0.9 -n 7 -M 2400 -d 0 -T 10...

zhengshimao

Hi! I am using cd-hit to cluster de novo repeats from repeatmodeler. I am thinking about ways to do more with the identified clusters than just keeping one representative. So...

schraderL

Functionality missing for -sf option in cd-hit-est

2

I ran the following command for cd-hit-est and got the expected two output files, so it ran successfully ./cd-hit-est -i /home/tsc7044/cd-hit-v4.8.1-2019-0228/soil_ntc04_processed.fasta -o soil_ntc04_cdhit99 -c 0.99 -n 11 -g 1 -d...

tcr0fts

Hi, I tried to use `make_multi_seq.pl` to generates separate fasta files for each cluster, but it didn't work. The command I used is: `make_multi_seq.pl raw_hifi_reads.fastq ../99.clstr 99_new 2` However, the...

WAining

Directory rather than a single file as an input?

1

How to provide cd-hit with a directory rather than a file as input? My purpose is to compare all the sequences in all fasta files in this directory against each...

neginmb