Platanus_B README.md

Description

Platanus_B is a de novo assembler for isolated bacterial genomes. The features of this tool are as follows: (1) It requires at least one Illuimina paired-end library. This library is useful for large-scale and/or high-resolution analysis. (2) It also can accept Oxford-Nanopore and/or PacBio long reads ("iterate" command). (3) Implementing the iteration of sequence-extensions, gap-closing and error-removals, it can archive assemblies with contiguity and accuracy for many cases. (4) As an utility function, it can combine multiple assemblies through the "combine" command.

Version

v1.3.2

Web site

http://platanus.bio.titech.ac.jp/

Author

Rei Kajitani at Tokyo Institute of Technology wrote key source codes.
Address for this tool: platanus@bio.titech.ac.jp

Requirements

• OpenMP

  • To compile the source code.

• Minimap2

  • https://github.com/lh3/minimap2
  • Included in this package.
  • Only required to use Oxford-Nanopore/PacBio long reads.

• Perl

  • To execute the scripts in this package, which .

Installation

Using Docker

docker pull rkajitani/platanus_b
docker run -it --rm -v $(pwd):/work -w /work rkajitani/platanus_b

Options of docker run can be modified according to users' environments and purposes (e.g., --rm and -v).

From source

make
cp platanus_b <installation_path>

Note that the absolute path of "sub_bin", which consists of Perl-scripts and minimap2 for "iterate" and "combine" commands, are written in the platanus_b executable. Please re-complile this if you move sub_bin to another directory. For macOS, please install OpenMP if a complilation fails. This can be installed using Homebrew with the command of "brew install libomp" or "brew install llvm".

Synopsis

Inputs

• Illumina paired-end: PE_1.fq PE_2.fq (mandatory)
• Oxford Nanopor long-reads: ONT.fq (optional)

Commands

platanus_b assemble -f PE_1.fq PE_2.fq 2>assemble.log
platanus_b iterate -c out_contig.fa -IP1 PE_1.fq PE_2.fq -ont ONT.fq 2>iterate.log

Final output

out_iterativeAssembly.fa

---

Contig assembly usage

Command

platanus_b assemble [OPTIONS] 2>log

Options

-o STR               : prefix of output files (default out, length <= 200)
-f FILE1 [FILE2 ...] : reads file (fasta or fastq, number <= 100)
-k INT               : initial k-mer size (default 32)
-K FLOAT             : maximum-k-mer factor (maximum-k = FLOAT*read-length, default  0.5)
-s INT               : step size of k-mer extension (>= 1, default 10)
-n INT               : initial k-mer coverage cutoff (default 0, 0 means auto)
-c INT               : minimun k-mer coverage (default 1)
-a FLOAT             : k-mer extension safety level (default 10.0)
-u FLOAT             : maximum difference for bubble crush (identity, default 0)
-d FLOAT             : maximum difference for branch cutting (coverage ratio, default 0.5)
-e FLOAT             : k-mer coverage depth (k = initial k-mer size specified by -k) of homozygous region (default auto)
-t INT               : number of threads (<= 100, default 1)
-m INT               : memory limit for making kmer distribution (GB, >=1, default 16)
-tmp DIR             : directory for temporary files (default .)
-kmer_occ_only       : only output k-mer occurrence table (out_kmer_occ.bin; default off)
-repeat              : mode to assemble repetitive sequences (e.g. 16s rRNA))

Input format:

Uncompressed and compressed (gzip or bzip2) files are accepted for -f option.

Outputs:

PREFIX_contig.fa
PREFIX_kmerFrq.tsv

PREFIX is specified by -o

Iteration of sequence-extension, gap-closeing and error-removal.

Command

platanus_b iterate [OPTIONS] 2>log

Options

-o STR                             : prefix of output file and directory (do not use "/", default out, length <= 200)
-c FILE1 [FILE2 ...]               : contig (or scaffold) file (fasta format)
-i INT                             : number of iterations (default 6)
-l INT                             : -l value of "scaffold" step
-u FLOAT                           : maximum difference for bubble crush (identity, default 0)
-ip{INT} PAIR1 [PAIR2 ...]         : lib_id inward_pair_file (reads in 1 file, fasta or fastq)
-IP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id inward_pair_files (reads in 2 files, fasta or fastq)
-op{INT} PAIR1 [PAIR2 ...]         : lib_id outward_pair_file (reads in 1 file, fasta or fastq)
-OP{INT} FWD1 REV1 [FWD2 REV2 ...] : lib_id outward_pair_files (reads in 2 files, fasta or fastq)
-ont FILE1 [FILE2 ...]             : Oxford Nanopore long-read file (fasta or fastq)
-p FILE1 [FILE2 ...]               : PacBio long-read file (fasta or fastq)
-gc FILE1 [FILE2 ...]              : Guiding contig file; i.e. other assemblies, synthetic long-reads or corrected reads (fasta or fastq)
-t INT                             : number of threads (default 1)
-m INT                             : memory limit for making kmer distribution (GB, >=1, default 1)
-tmp DIR                           : directory for temporary files (default .)
-sub_bin DIR                       : directory for binary files which platanus_b use internally (e.g. minimap2) (default compilation-dir/sub_bin)
-keep_file                         : keep intermediate files (default, off)
-trim_overlap                      : trim overlapping edges of scaffolds (default, off)

Input format:

Uncompressed and compressed (gzip or bzip2) files are accepted for -c, -ip, -IP, -op, -OP, -p, -x and -X option.

Outputs:

PREFIX_iterativeAssembly.fa (including sequences below)

PREFIX is specified by -o

---

Notes

• Options related to run time Although -t (number of threads) of all commands and -m (memory amount) of the "assemble" command are not mandatory to run, it is recommended to set the values adjusting your machine-environment. These options may severely effect the run time.
  e.g.,
  Available number of threads and memory amount are 4 and 16GB, respectively.
  -> -t 4 -m 16

• Compressed input files Both uncompressed and compressed (gzip or bzip2) FASTA/FASTQ files are accepted. Formats are auto-detected. Internally, "file -bL", "gzip -cd" and "bzip2 -cd" commands, which can be used in most of the UNIX OSs, are utilized.

• Paired-end (mate-pair) input
  The "phase" and "consensus" accept paired-end and/or mate-pair libraries. Paired libraries are classified into "inward-pair" and "outward-pair" according to the sequence direction. For file formats, separate and interleaved files can be input through -IP (-OP) and -ip (-op) options, respectively.

Inward-pair (usually called "paired-end", accepted in options "-IP" or "-ip"):

FWD --->
    5' -------------------- 3'
    3' -------------------- 5'
                    <--- REV 

Outward-pair (usually called "mate-pair", accepted in options "-OP" or "-op"):

                    ---> REV 
    5' -------------------- 3'
    3' -------------------- 5'
FWD <---

Example inputs:

Inward-pair (separate, insert=300)   : PE300_1.fq PE300_2.fq
Inward-pair (interleaved, insert=500): PE500_pair.fq
Outward-pair (separate, insert=2k)   : MP2k_1.fa MP2k_2.fq

Corresponding options:

-IP1 PE300_1_pair.fq PE300_2.fq \
-ip2 PE500_pair.fq \
-OP3 MP2k_1.fq MP2k_2.fq