ABySS

Contact owners and managers

1–30 of 1268

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

Check out our github page for ABySS documentation and frequently asked questions: https://github.com/bcgsc/abyss

0 selected

David Maddison, Lauren Coombe4

12/18/23

ABySS versus CLC: ABySS options to perform as well as CLC?

Hi David, Thanks for confirming! Yes, totally understand that you have to deal with what you can get

unread,

ABySS versus CLC: ABySS options to perform as well as CLC?

Hi David, Thanks for confirming! Yes, totally understand that you have to deal with what you can get

12/18/23

Pavle Eric, Lauren Coombe9

9/7/23

little help with abyss assembler

Hi Pavle, Hmm that's an interesting one - I haven't seen that error before. Good to know that

unread,

little help with abyss assembler

Hi Pavle, Hmm that's an interesting one - I haven't seen that error before. Good to know that

9/7/23

8/9/23

Hi Pavle, We require moderation of posts before they are available on the google group, so your

unread,

Hi Pavle, We require moderation of posts before they are available on the google group, so your

8/9/23

Sabrin Abdelghany, … Lauren Coombe4

9/7/22

Fwd: no abyss-pe.Makefile in (/.conda/envs/abyss/bin)

Hi Asad, Thank you for mentioning that! Yes, there are multiple options for running ABySS, including

unread,

Fwd: no abyss-pe.Makefile in (/.conda/envs/abyss/bin)

Hi Asad, Thank you for mentioning that! Yes, there are multiple options for running ABySS, including

9/7/22

Amin Ghane, Lauren Coombe4

7/22/22

Using ABySS to assemble kmers into contigs

Hi Amin, If you can't update to the newest version, do try using the de Bruijn graph mode of

unread,

Using ABySS to assemble kmers into contigs

Hi Amin, If you can't update to the newest version, do try using the de Bruijn graph mode of

7/22/22

Pawarut NARONGPUN, Lauren Coombe2

5/27/22

Average coverage

Hi Pawarut, Could you clarify a bit what you're looking to find? The coverage of the sequencing

unread,

Average coverage

Hi Pawarut, Could you clarify a bit what you're looking to find? The coverage of the sequencing

5/27/22

Paige M., johnath...@gmail.com13

3/8/22

Hi Paige, I'm always happy to help. Best of luck win your endeavor. Using bioinformatics software

unread,

Hi Paige, I'm always happy to help. Best of luck win your endeavor. Using bioinformatics software

3/8/22

Melissa hpy, Lauren Coombe4

10/7/21

Empty output sealer-abyss

Hi Melissa, That indicates that the program is still adding your input reads to the Bloom filter data

unread,

Empty output sealer-abyss

Hi Melissa, That indicates that the program is still adding your input reads to the Bloom filter data

10/7/21

10/5/21

Hi I´m running sealer-abyss but I get empty outputs. Since I start to run the code the folowing files

unread,

Hi I´m running sealer-abyss but I get empty outputs. Since I start to run the code the folowing files

10/5/21

Anna Gregory, Lauren Coombe4

5/4/21

The file cannot be accessed by the system.

Hi Anna, Excellent! Glad everything's working for you :) Thank you for your interest in ABySS!

unread,

The file cannot be accessed by the system.

Hi Anna, Excellent! Glad everything's working for you :) Thank you for your interest in ABySS!

5/4/21

Nayeli Gutiérrez, Lauren Coombe4

1/25/21

Scaffolding with linked reads

Hi Nayel, From your script, it appears that you are using quite an old version of ABySS (2.0.2)? The

unread,

Scaffolding with linked reads

Hi Nayel, From your script, it appears that you are using quite an old version of ABySS (2.0.2)? The

1/25/21

Nayeli Gutiérrez, Lauren Coombe2

1/21/21

error: sequence with ID `GWNJ-7/1' is empty

Hi Nayeli, Have you taken a look at that sequence? Is it in fact empty? You should make sure that any

unread,

error: sequence with ID `GWNJ-7/1' is empty

Hi Nayeli, Have you taken a look at that sequence? Is it in fact empty? You should make sure that any

1/21/21

Allison S, Lauren Coombe2

4/22/20

How does ABySS determine "fragment size"

HI Allison, We answered your question on our github page: https://github.com/bcgsc/abyss/issues/170

unread,

How does ABySS determine "fragment size"

HI Allison, We answered your question on our github page: https://github.com/bcgsc/abyss/issues/170

4/22/20

Joy Ding, Lauren Coombe6

4/21/20

Contigs and scaffolds are identical

Hi Joy, abyss-fac by default uses a length threshold of 500bp for calculating it's statistics. If

unread,

Contigs and scaffolds are identical

Hi Joy, abyss-fac by default uses a length threshold of 500bp for calculating it's statistics. If

4/21/20

Arsalan Emami-Khoyi, Lauren Coombe4

2/25/20

abyss assembly and bubbles

Many thanks Lauren! On Monday, February 24, 2020 at 9:08:52 PM UTC+2, Lauren Coombe wrote: To clarify

unread,

abyss assembly and bubbles

Many thanks Lauren! On Monday, February 24, 2020 at 9:08:52 PM UTC+2, Lauren Coombe wrote: To clarify

2/25/20

Peiwen Li, Johnathan Wong2

2/24/20

ABySS 2.2.3 Bloom filter false positive rate

For posterity: Answered in https://github.com/bcgsc/abyss/issues/311 On Monday, 20 January 2020 17:05

unread,

ABySS 2.2.3 Bloom filter false positive rate

For posterity: Answered in https://github.com/bcgsc/abyss/issues/311 On Monday, 20 January 2020 17:05

2/24/20

Safiqul Islam, Johnathan Wong2

2/24/20

recipe for target

Hello, Can you `ls` your directory and show me what you have? And what is the memory of your system?

unread,

recipe for target

Hello, Can you `ls` your directory and show me what you have? And what is the memory of your system?

2/24/20

Ravi Sachidanandam

2/18/19

Is it possible to just assemble single end reads from a fasta file

I am trying to assemble single end reads using just se='file.fa" actual command is abyss-pe

unread,

Is it possible to just assemble single end reads from a fasta file

I am trying to assemble single end reads using just se='file.fa" actual command is abyss-pe

2/18/19

Prasoon Thakur, Alejandro Sanchez2

12/18/18

help regarding abyss assembly

Hi, The unitigs.fa should be the contigs that you could scaffold. Although, if they contain Ns then

unread,

help regarding abyss assembly

Hi, The unitigs.fa should be the contigs that you could scaffold. Although, if they contain Ns then

12/18/18

9/9/18

Re: ABySS compiling error <Semaphore.h> vs <semaphore.h> in NTFS file system

Unable to display this message Click here to open this message SMTP message delayed: hrbq - Date: 09/

unread,

Re: ABySS compiling error <Semaphore.h> vs <semaphore.h> in NTFS file system

Unable to display this message Click here to open this message SMTP message delayed: hrbq - Date: 09/

9/9/18

7/31/18

ABySS compiling error <Semaphore.h> vs <semaphore.h> in NTFS file system

Hello there, I am using Win10 WSL Ubuntu and I am trying to compiling ABySS from source (I need ak

unread,

ABySS compiling error <Semaphore.h> vs <semaphore.h> in NTFS file system

Hello there, I am using Win10 WSL Ubuntu and I am trying to compiling ABySS from source (I need ak

7/31/18

Philippine De Boissel, Ben Vandervalk2

7/13/18

ABySS want contigs < 500 pb - how to change parameter?

Hi Phillipine, You can report stats with a minimum sequence length threshold of 100 bp by running `

unread,

ABySS want contigs < 500 pb - how to change parameter?

Hi Phillipine, You can report stats with a minimum sequence length threshold of 100 bp by running `

7/13/18

leonardo alves, Ben Vandervalk5

5/3/18

A question on how abyss-pe manages to find the library files

That is alright. Thank you Ben! Em quinta-feira, 3 de maio de 2018 12:52:28 UTC-3, Ben Vandervalk

unread,

A question on how abyss-pe manages to find the library files

That is alright. Thank you Ben! Em quinta-feira, 3 de maio de 2018 12:52:28 UTC-3, Ben Vandervalk

5/3/18

Arthur Pastuer, … Ben Vandervalk6

3/29/18

compiling with google sparsehash 1.8.1

I've seen this error before... try connecting `--with-sparsehash` and the path with an equals

unread,

compiling with google sparsehash 1.8.1

I've seen this error before... try connecting `--with-sparsehash` and the path with an equals

3/29/18

jca...@gmail.com, … Ben Vandervalk6

3/28/18

abyss performance

Oh, okey! Thank you very much for the suggestions. I will test these new settings and I will let you

unread,

abyss performance

Oh, okey! Thank you very much for the suggestions. I will test these new settings and I will let you

3/28/18

Vid, Ben Vandervalk6

11/24/17

ERROR 127: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory

mode* On Fri, Nov 24, 2017 at 3:18 PM, Ben Vandervalk <ben....@gmail.com> wrote: No, you

unread,

ERROR 127: ABYSS-P: error while loading shared libraries: libmpi.so.40: cannot open shared object file: No such file or directory

mode* On Fri, Nov 24, 2017 at 3:18 PM, Ben Vandervalk <ben....@gmail.com> wrote: No, you

11/24/17

Vid, Ben Vandervalk3

11/24/17

Can't find ABYSS-P after compiling

installed* On Fri, Nov 24, 2017 at 2:56 PM, Ben Vandervalk <ben....@gmail.com> wrote: Hi Vid,

unread,

Can't find ABYSS-P after compiling

installed* On Fri, Nov 24, 2017 at 2:56 PM, Ben Vandervalk <ben....@gmail.com> wrote: Hi Vid,

11/24/17

Sagar, Ben Vandervalk3

7/10/17

Assembly size reduced after Sealer

Thank you very much for the quick reply. This makes perfect sense. On Friday, July 7, 2017 at 2:17:33

unread,

Assembly size reduced after Sealer

Thank you very much for the quick reply. This makes perfect sense. On Friday, July 7, 2017 at 2:17:33

7/10/17

Dr. Gaurav Sablok, … Elena Bushmanova21

6/2/17

Assembling single end reads in abyss

"sed '$d' reads.fq > reads.removed.fq" helps me! четверг, 19 июня 2014 г., 2:00:

unread,

Assembling single end reads in abyss

"sed '$d' reads.fq > reads.removed.fq" helps me! четверг, 19 июня 2014 г., 2:00:

6/2/17

aquat...@g.hmc.edu, … Ben Vandervalk5

4/6/17

abyss-pe failure after files read

Oops... https://gist.github.com/quattrinia/b7bc0e157ec48fa6f3db3805b9ff1a02 On Thursday, April 6,

unread,

abyss-pe failure after files read

Oops... https://gist.github.com/quattrinia/b7bc0e157ec48fa6f3db3805b9ff1a02 On Thursday, April 6,

4/6/17

Search

Clear search

Close search

Google apps

Main menu