help regarding abyss assembly

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Prasoon Thakur

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Dec 18, 2018, 11:17:16 AM12/18/18
to ABySS

Hi,


I have paired DNA-seq data of some protista. I tried to do assembly using the abyss 2.1.1 after trimming using Trimmomatic. Trimmomatic preprocessed reads into Paired end reads (Forward and Reverse) and unpaired reads from each file that I have considered as single end reads for abyss assembly.


Used command for the abyss


for k in {150..250..10}; do mkdir k$k; cd k$k; abyss-pe k=$k name=1604 pe='../protista_forward_paired.fastq ../protista_reverse_paired.fastq' se='../protista_forward_unpaired.fastq ../protista_reverse_unpaired.fastq'; cd ..; done

I got three contig files like protista_contig-1.fa, protista_contig-2.fa, protista_contig-3.fa.


complete list of output :


coverage.hist, protista-bubbles.fa, protista-1.fa, protista-1.dot, protista-1.path, protista-2.dot1, protista-2.fa, protista-2.dot, protista-3.dot, protista-2.path, protista-3.fa, protista-indel.fa, protista-unitigs.fa , protista-3.fa


I am not sure which config file I should use for further analysis including scaffolding. Could someone please help me with this.


Thank you very much in advance.

Alejandro Sanchez

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Dec 18, 2018, 12:54:11 PM12/18/18
to Prasoon Thakur, ABySS
Hi,

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

Only if you have a library with a long insert size, it will be worthy to rescaffold, otherwise it wouldn't make a big difference.

There's lots of post assembly things that you can do like check for misassemblies and fill gaps. There are several tools to do so but REAPR and GapFiller are my favorites, respectively.

Cheers

Cheers!


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