Using minion reads with LAST

[lfaller]

Hello all,

I am interested in comparing two canu assemblies using LAST. The reference assembly has 25 contigs and the query assembly has 21 contigs. The assemblies are for GC rich bacteria (same species but different strains, so I expect them to be somewhat similar).

I followed the instructions provided here: https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md

However, the output I get seems to just be the comments:

# make an index using the WT strain
~/bin/lastdb -P40 -uNEAR -R01 WT_db reference.contigs.fasta

# align mutant against the WT strain
~/bin/lastal -P40 WT_db query.contigs.fasta
# LAST version 885
#
# a=21 b=9 A=21 B=9 e=60 d=0 x=59 y=44 z=59 D=1e+06 E=5e+11
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.36661 j=3 Q=0
# WT_db
# Reference sequences=25 normal letters=0
# lambda=0.228526 K=0.433378
#
#    A  C  G  T
# A  6 -18 -18 -18
# C -18  6 -18 -18
# G -18 -18  6 -18
# T -18 -18 -18  6
#
# Coordinates are 0-based.  For - strand matches, coordinates
# in the reverse complement of the 2nd sequence are used.
#
# name start alnSize strand seqSize alignment
#
# batch 0
# Query sequences=21

I also tried submitting these two assemblies to the web service but received the message "no alignments were found":

I am new to LAST. Could it be that my sequences are too similar? Is this an appropriate problem for LAST?

Thanks for any advice! ~Lina

[mcfrith]

Hi Lina,

I'm afraid this reply is both late and useless.

I think it's an appropriate problem, and "too similar" should not matter. I'm surprised you're getting no alignments. The only way to figure this out is if you can share your sequences.

(I would recommend also using last-split, and probably last-train. But "no alignments" suggests some deeper problem.)

Have a nice day, Martin

[lfaller]

Thank you for the quick reply! If you don't mind taking a look at my sequences, I will send them to you via email.

Best, ~Lina