Introduction

The StriDe Assembler integrates string and de Bruijn graph by decomposing reads within error-prone regions, while extending paire-end read into long reads for assembly through repetitive regions. The entire implementation is done by revising Simpson's SGA components for our own purpose, porting Li's ropebwt2 for FM-index construction, and adding key components of this assembler.

Download binary version

Download the binary file called StriDe_Linux64bit_v1.0.tar.gz (compiled on linux 64bit) and type

tar zxvf StriDe_Linux64bit_v1.0.tar.gz

Compile by yourself

To compile StriDe assembler in your specific environment, type

  1. ./autogen.sh 
  2. ./configure
  3. make

An executable program called stride will be found under the StriDe folder.

Execution

The program can be executed in all-in-one mode or step-by-step mode, depending on the commands specified.

All-in-one Commands (experimental):

  all	  Perform error correction, long-read generation, overlap computation, and assembly in one run

Step-by-step Commands:

  preprocess  filter and quality-trim reads
  index       build FM-index for a set of reads
  correct     correct sequencing errors in reads 
  fmwalk      merge paired reads into long reads via FM-index walk
  filter      remove redundant reads from a data set
  overlap     compute overlaps between reads
  assemble    generate contigs from an assembly graph

For instance, given two pair-end reads data sets in fastq format (A_R1.fq, A_R2.fq), simply type

  stride all A_R1.fq A_R2.fq

The entire preprocess, index, correction, fmwalk/decomposition, ... will be performed.

For multiple PE libraries, each pair of reads of the same library should be appeneded. e.g., two PE lib of insert 200bp and 600bp with max read length 300bp.

  ./stride all -r 300 -i 600 insert_200_1.fastq insert_200_2.fastq insert_600_1.fastq insert_600_2.fastq

Example of a Step-by-step script

  stride preprocess --discard-quality -p 1 A_R1.fq A_R2.fq -o reads.fa
  stride index -a ropebwt2 -t 30 reads.fa
  stride correct -a overlap -t 30 -k 31 -x 3 reads.fa -o READ.ECOLr.fasta
  stride index  -t 30 READ.ECOLr.fasta
  stride fmwalk -m 80 -M 95 -t 30 -L 32 -I 400 -k 31 -p READ.ECOLr READ.ECOLr.fasta
  cat READ.ECOLr.merge.fa READ.ECOLr.kmerized.fa >merged.fa
  stride index -t 30 merged.fa
  stride filter -t 30 --no-kmer-check merged.fa
  stride overlap -m 30 -t 30 merged.filter.pass.fa
  stride assemble -k 31 -t 3 -p READ.ECOLr -r 100 -i 200 merged.filter.pass.asqg.gz