[CD-HIT] CD-HIT Project Web Page

[Dan Bolser]

Thanks Kely,

Archiving this kind of information is exactly what the mailing list is for :-)

Cheers,
Dan.


2009/10/21 Raquel Norel <rn98 at columbia.edu>:
> Hi Dan,
>                the latest, not beta version of cd-hit is the 3.1.2 which
> does not have the -u option.
> I contacted cd-hit author and he explained to me how to proceed.
> Please see below
> Thanks
> Kely
>
> Hi,
>
> -u option is no longer available. The incremental update can be performed by
> combine cd-hit and cd-hit-2d programs, which is more efficient and more
> reliable.
>
> This can be found in the cd-hit user's guide, I copy it here:
>
> Incremental clustering
>
> It is easy to make incremental update with cd-hit /cd-hit-2d. For example:
>
> nr is the nr database of last month
>
> month is the new sequences of nr of this month
>
> In last month, you ran:
>
> cd-hit -i nr -o nr90 -c 0.9 -n 5
>
> This month, you can run incremental clustering
>
> cd-hit-2d -i nr90 -i2 month -o month-new -c 0.9 -n 5
>
> cd-hit -i month-new -o month90 -c 0.9 -n 5
>
> cat month90 >> nr90
>
> clstr_merge.pl
>
> nr90.clstr month-new.clstr > temp.clstr
>
> cat temp.clstr month90.clstr > this_month_nr90.clstr
>
> This approach is much faster than runing from scratch. It also preserves
> stable cluster structure.
>
> Let me know whether this works for you or you find any problem with this
> option.
>
> Thanks,
>
> Weizhong,
>
> On Wed, Oct 21, 2009 at 8:57 AM, Dan Bolser <dmb at bioinformatics.org> wrote:
>>
>> Hi Kely,
>>
>> There was a new release of CD-HIT recently, can you check if the
>> incremental updates are now available?
>>
>> I have CC'ed this reply to the cd-hit mailing list. Please feel free
>> to join that list if you have any further questions:
>>
>> http://www.bioinformatics.org/mailman/listinfo/cd-hit-l
>>
>>
>> All the best,
>> Dan.
>>
>>
>>
>>
>> 2009/10/14 Raquel Norel <rn98 at columbia.edu>:
>> > Hi,
>> >   do you know is the option -u was removed from version 3.1.2 from
>> > cd-hit?
>> > in version 3.1.1 is working fine.
>> > So no incremental updates?
>> > Thanks
>> > Kely
>> >
>
>