Introduction

NECAT is an error correction and assembly tool for Nanopore long noisy reads.

Installation

We currently only provide executable binaries, which can be downloaded and installed in the following way.

$ wget https://github.com/xiaochuanle/NECAT/releases/download/v0.01/necat_20190307_linux_amd64.tar.gz
$ tar xzvf necat_20190307_linux_amd64.tar.gz
$ export PATH=$PATH:$(pwd)/NECAT/Linux-amd64/bin

After decompression, all the executable files can be found in NECAT/Linux-amd64/bin. The third line above is used for adding NECAT/Linux-amd64/bin to the system PATH.

Quick Start

Step 1: Create a config file

Create a config file template using the following command:

$ necat.pl config ecoli_config.txt

The template looks like

PROJECT=
ONT_READ_LIST=
GENOME_SIZE=
THREADS=4
MIN_READ_LENGTH=3000
OVLP_FAST_OPTIONS="-n 500 -z 20 -b 2000 -e 0.5 -j 0 -u 1 -a 1000"
OVLP_SENSITIVE_OPTIONS="-n 500 -z 10 -e 0.5 -j 0 -u 1 -a 1000"
CNS_FAST_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0"
CNS_SENSITIVE_OPTIONS="-a 2000 -x 4 -y 12 -l 1000 -e 0.5 -p 0.8 -u 0"
TRIM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 1 -a 400"
ASM_OVLP_OPTIONS="-n 100 -z 10 -b 2000 -e 0.5 -j 1 -u 0 -a 400"
NUM_ITER=2
CNS_OUTPUT_COVERAGE=45
CLEANUP=0
USE_GRID=false
GRID_NODE=0
FSA_OL_FILTER_OPTIONS="--max_overhang=-1 --min_identity=-1 --coverage=40"
FSA_ASSEMBLE_OPTIONS=""
FSA_CTG_BRIDGE_OPTIONS="--dump --read2ctg_min_identity=80 --read2ctg_min_coverage=4 --read2ctg_max_overhang=500 --read_min_length=5000 --ctg_min_length=1000 --read2ctg_min_aligned_length=5000 --select_branch=best"

Filling and modifying the relative information, we have

PROJECT=ecoli
ONT_READ_LIST=read_list.txt
GENOME_SIZE=4600000
THREADS=20
MIN_READ_LENGTH=3000
  ......

read_list.txt in the second line above contains the full paths of all read files. It looks like

$ cat read_list.txt
/share/home/chuanlex/xiaochuanle/data/testdata/tomato/20161027_Spenn_001_001_all.fastq
/share/home/chuanlex/xiaochuanle/data/testdata/tomato/20161101_Spenn_002_002_all.fastq
/share/home/chuanlex/xiaochuanle/data/testdata/tomato/20161103_Spenn_003_003_all.fastq
/share/home/chuanlex/xiaochuanle/data/testdata/tomato/20161108_Spenn_004_004_all.fastq
/share/home/chuanlex/xiaochuanle/data/testdata/tomato/20161108_Spenn_004_005_all.fastq

Step 2: Correct raw reads

Correct the raw noisy reads using the following command:

$ necat.pl correct ecoli_config.txt

The corrected reads is ./ecoli/1-consensus/cns_iter${NUM_ITER}/cns.fasta.
The extracted longest 45x corrected reads is ./ecoli/1-consensus/cns_final.fasta

Step 3: Assemble contigs

After correcting the raw reads, we assemble the contigs using the following command. If the correcting-step is not done, the command automatically runs the correcting-step first.

$ necat.pl assemble ecoli_config.txt

The assembled contigs is ./ecoli/4-fsa/contigs.fasta.

Step 4: Bridge contigs

After assembling the contigs, we run the bridging-step using the following command. The command checks and runs the preceding steps first.

$ necat.pl bridge ecoli_config.txt

The bridged contigs is ./ecoli/6-bridge_contigs/bridged_contigs.fasta.