hillerlab/iterativeerrorcorrection

Iterative error correction of long reads

iterativeerrorcorrection's Issues

Versioned release package for SGA-ICE

I'm working to make SGA-ICE available on Bioconda.

Please refer. -> https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release

I need your help creating a versioned release to use for the Bioconda recipe. Once SGA-ICE is added to Bioconda, it'll also be made available as a Docker container from Biocontainers, and as a Singularity image from the Galaxy Project. The Bioconda bot will also recognize future releases and automatically update the recipe.

Please let me know

Thanks
Jay

Paired-end support

Hi,
Does SGA-ICE support paired-end files and if yes then is it enough just to do SGA-ICE.py /path/to/fastq/data/ -t 8?

Thank you in advance.

Best wishes,

Michal

SGA-ICE install

Hi,

I tried to install sga-ice, but when i try to excecute , getting below error

./SGA-ICE.py -h
File "/data/install/sga-ice/IterativeErrorCorrection-1.0/./SGA-ICE.py", line 35
    print '### Input directory is:', args.inputDir
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?

Please advice

Thanks
Jay

choosing kmer for down stream analyse

Hi,
I ran SGA-ICE and it chose 40, 70, 100 as kmer for a paired read length of 150.

Which kmer should I choose for downstream analyse e.g. for sga filter?

Thank you in advance.

Best wishes,

Mic

Disk use limitation

Hi,
When SGA-ICE is run using multiple-kmer values it saves each intermediate file to the tmp directory. The cleanup option only seems to remove the files at the very end of the run. If the original fastq (not gzipped, is that a limitation of SGA-ICE or SGA?) is large and paired, so 2 40G files, saving the intermediate files becomes a space issue. For example, a kmer option of 50, 100, 150, 200 would produce 400G in intermediate files. I edited the bash file to include 'rm' to remove the intermediate files and it seems to have worked out OK. Do you see any issue with adding the 'rm' line? I added it before the "build index" where k50 was corrected to k100, then I removed k50 before the index was built on k100.

All reads must have a unique identifier

Hi
I have received the following error:

[sga::overlap] parsing file reads.pp.ec.filter.pass-thread11.hits.gz
Error: Attempted to insert vertex into graph with a duplicate id: @NS500334:63:HF2WTBGXY:3:13401:17773:1683
All reads must have a unique identifier

with using the following commands:

#SGA-ICE.py `pwd` -t 12
#./runMe.sh

cd ec/

IN1=out_NtC_001879-1.final.ecOv.fq.fasta
IN2=out_NtC_001879-2.final.ecOv.fq.fasta

#
# Parameters
#

# The number of threads to use
CPU=12

# The minimum length of contigs to include in a scaffold
MIN_CONTIG_LENGTH=200

#
# Preprocessing
#

# Preprocess the data to remove ambiguous basecalls
cat out_NtC_001879-*.final.ecOv.fq.fasta > reads.pp.ec.fasta

#
# Primary (contig) assembly
#

# Index the corrected data.
sga index -a ropebwt -t $CPU reads.pp.ec.fasta

# Remove exact-match duplicates and reads with low-frequency k-mers
sga filter --homopolymer-check --low-complexity-check -t $CPU reads.pp.ec.fasta

# Compute the structure of the string graph
sga overlap -t $CPU reads.pp.ec.filter.pass.fa

However, checking FASTQ files I could not discover this duplication:

> grep "@NS500334:63:HF2WTBGXY:3:13401:17773:1683" out_NtC_001879-1.fq 
@NS500334:63:HF2WTBGXY:3:13401:17773:1683 1:N:0:GATCAG
> grep "@NS500334:63:HF2WTBGXY:3:13401:17773:1683" out_NtC_001879-2.fq 
@NS500334:63:HF2WTBGXY:3:13401:17773:1683 2:N:0:GATCAG

Did I do anything wrong?

Best wishes,

Micha;