documentation for ABySS

harrb · 11-23-2010, 08:45 AM

Hello,

I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
I have 4 questions:

1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?

2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.

3) What is the number of mismatches allowed in a read to still be assembled to a contig?

4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)

>29036 60 1326
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
>29037 61 114
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
>29038 62 268
TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
>29039 60 1139
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
>29040 61 51
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
>29041 60 13
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
>29042 61 183
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
>29043 61 44
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
>29044 61 70
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
>29045 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
>29046 69 34
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
>29047 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA

It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?

Thanks so much for your help!

Bioinfo · 11-23-2010, 09:18 AM

Quote:

Originally Posted by harrb

Hello,

I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output.
I have 4 questions:

1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained?

2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode.

3) What is the number of mismatches allowed in a read to still be assembled to a contig?

4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa)

>29036 60 1326
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG
>29037 61 114
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG
>29038 62 268
TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG
>29039 60 1139
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG
>29040 61 51
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG
>29041 60 13
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT
>29042 61 183
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG
>29043 61 44
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG
>29044 61 70
CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG
>29045 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA
>29046 69 34
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA
>29047 69 20
GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA

It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig?

Thanks so much for your help!

Hi,
hope this paper may helps you..
best

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11-23-2010, 08:45 AM	#1
harrb Junior Member Location: Germany Join Date: Feb 2008 Posts: 5	documentation for ABySS Hello, I am a new user of ABySS. I have 50 Million Solexa 100bp paired-end transcriptome reads that I am intending to assemble de novo. Velvet could not handle my dataset, but my first run with ABySS worked. However, I have a hard time understanding the output. I have 4 questions: 1) I could not find any documentation on the output files created. Can someone maybe direct me to a page where the various files are explained? 2) I also do not quite understand if ABySS considers the paired end reads for the alignment or not. Does someone know? I have run the "pe" mode. 3) What is the number of mismatches allowed in a read to still be assembled to a contig? 4) below I pasted a few contigs from the outfile that Abyss has created (i.e. xxx_contigs.fa) >29036 60 1326 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTG >29037 61 114 CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGTTG >29038 62 268 TCGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTGTG >29039 60 1139 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTG >29040 61 51 CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCCG >29041 60 13 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTT >29042 61 183 CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGGTG >29043 61 44 CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCCG >29044 61 70 CGGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTTTG >29045 69 20 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGGCTCATAAATGCA >29046 69 34 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTCATAAATGCA >29047 69 20 GGCTCGAGGGTATCTAGAGTCACCAAAGCTGCCGGGCGGGCCCGGGGTGGGTTTGGTCTTGTAAATGCA It is quite clear that these reads are identical with the exception of a few single base mismatchs. Why are they not merged into a single contig? Thanks so much for your help! Last edited by harrb; 11-23-2010 at 08:58 AM.