For ABySS, I have a question for file that the assembly will go to

Question

[flavobacteria]

Assembling a paired-end library

To assemble paired reads in two files named reads1.fa and reads2.fa into contigs in a file named ecoli-contigs.fa, run the command:

abyss-pe name=ecoli k=64 in='reads1.fa reads2.fa' The parameter in specifies the input files to read, which may be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format and compressed with gz, bz2 or xz and may be tarred. The assembled contigs will be stored in ${name}-contigs.fa.

A pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.

Reads without mates should be placed in a file specified by the parameter se (single-end). Reads without mates in the paired-end files will slow down the paired-end assembler considerably during the abyss-fixmate stage.

My question is:

Does the "ecoli" file is made before we run this command?

[GenoMax]

If this is really E coli data then you may want to look at SPAdes as a good alternative assembler.

[st.ph.n]

It is not made before you run the command. The outputted assembly will be in the -contigs.fa file, with the prefix of ecoli, hence the flag for name. There should also be a scaffolds file.

[flavobacteria]

Thank you for replying. My data set is really large (fungi genome). what I am asking is where really "ecoli " here comes from? We give? if we give the name, how the software knows where it locates (or simply the Abyss think it should be the same folder in the "in" file. Thank you again.

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

As described by @st.ph.n, ecoli is an example prefix designation. You can say name=my_fungus and presumably the assembly file when ready will have a name like my_fungus-contigs.fa.

[st.ph.n]

The authors are using the 'ecoli' output prefix as an example. You can put anything you want after in the flag 'name=' (ex. name=myassembly), and it will be outputted as 'myassembly-contigs.fa'. If you want to specify the output path, use the flag '-C' with the path you want following it. Please refer to the abyss README.