FixAME is a program for finding and fixing local assembly errors, as well as identifying whether these errors are possible chimeras.
First of all, you need to make sure all dependencies are installed at your $PATH
samtools v.1.12+
bcftools v.1.12+
BBMAP -- specially bbmap.sh and filterbyname.sh (it needs openjdk-7+)
-- Python 3.6+ and the dependecies
pysam v.0.15.4+
xopen v.0.9.0
pandas v.1.0.3+
Biopython v.1.77
regex
After that you can clone this repository to the desired location
git clone https://github.com/LiviaMoura/FixAME.git
If you don't want trouble and you want to make sure it'll work, we created a Dockerfile
docker build -t lmoura/fixame:1.0.0 -f Dockerfile .
or you can pull the docker image at
docker pull livmoura/fixame:1.0.0
All you need to run FixAME is a sample or a folder with bins with extension .fa|.fasta|.fna and a pair-ended reads (R1 and R2)
FixAME ignores fasta sequences smaller than 1000bp by default (800bp minimum). Theses sequences won`t be extended or have the errors located.
FixAME CAN'T deal with bins named using the same name differing with .1, .2, .3|.a, .b, .c| etc (ex.: bin.1, bin.2, bin.3)
FixAME.py --fasta sample.fasta -r1 R1.fastq -r2 R2.fastq --output_dir THIS_FOLDER
FixAME.py --bins THIS_FOLDER_CONTAINS_BINS -r1 R1.fastq -r2 R2.fastq --output_dir THIS_FOLDER
If you don't want to run the fixing on the found errors, you can only run the error_finder step. This is return only the local assembly errors that FixAME could identify.
FixAME.py error_finder -f sample.fa -r1 R1.fastq -r2 R2.fastq -o TEST_FOLDER