gsassembler.

[sharagii]

I had brought gsassembler for assembling the large fata files that i had.

I had the user manual but it was not 100% helpful...

can some one specify me how to write runAssembly command for assembling the fasta file...

runAssembly -o readfastafile

[westerman]

I had brought gsassembler for assembling the large fata files that i had.

I had the user manual but it was not 100% helpful...

can some one specify me how to write runAssembly command for assembling the fasta file...

runAssembly -o readfastafile

I actually find the Newbler documentation to be one of the better ones.

The short answer is to put the name of your Fasta file at the end of your command; e.g.,

runAssembly -o readfastafile my_sequences.fasta

Some other options I find helpful include:

# Newbler options:
# -nobig no ace files
# -m keep all in memory
# -ud treat each read separately; do not group
# -ml minimum overlap
# -mi minimum identity
# -g produce contig graph
# -consed produce consed files
# -large for large complex datasets
# -vt vector trim (primers, adapters, cloning vectors)
# -vs vector screen (contamination)
# -e expected depth of coverage