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TUTORIAL.md

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The Trans-ABySS package has 2 main applications:

  1. transabyss - RNAseq assembler at a single k-mer size
  2. transabyss-merge - merge multiple assemblies from (1)

Content:

PART 1. Assembly with transabyss

PART 2. Merging assemblies with transabyss-merge

Please use our Google Group [email protected] for discussions and support. Existing topics can be viewed at https://groups.google.com/d/forum/trans-abyss.

You may also create issues on our GitHub repository at https://github.com/bcgsc/transabyss/issues.

PART 1. Assembly with transabyss

[1.1] Usage
transabyss --help
[1.2] Running transabyss
transabyss --se reads.fq

See below for assembling single-end reads and/or pair-end reads.

[1.3] Input reads

Supported formats are compressed (gzip/bzip) FASTQ/FASTA/SAM/QSEQ or BAM files.
Paired-end reads in FASTQ/A can be interleaved or in separate files. Paired-end reads in FASTQ/A must have the suffixes /1 or /2 in the read name.

Use options --se and --pe to specify the path(s) of single-end reads and paired-end reads, respectively. Example usages:

combination reads for sequence content reads for paired-end linkage assembly
--se r.fq r.fq none single-end
--pe r.fq r.fq r.fq paired-end
--se SE.fq --pe PE.fq SE.fq PE.fq paired-end
--se SE.fq PE.fq --pe PE.fq SE.fq, PE.fq PE.fq paired-end
[1.4] Output assembly path

default: ./transabyss_2.0.0_assembly/transabyss-final.fa

Use options --name and --outdir to change the output directory and assembly name.

[1.5] k-mer size

default: 32

Use option --kmer to adjust the k-mer size. k=32 has a good trade-off for assembling both rare and common transcripts. Using larger k-mers improve the assembly quality of common transcripts and transcripts with repetitive regions, but the assembly of rare transcripts may suffer.

[1.6] MPI and multi-threading

default: no mpi processes; singe-threaded

Use option --threads to specify the number of threads. Use option --mpi to specify the number of MPI processes.

Only the first stage of assembly (de Bruijn graph) could benefit from MPI; all remaining stages may be multi-threaded.

[1.7] Strand-specific assembly

Use option --SS to indicate that input reads are strand-specific. Strand-specific reads are expected to have /1 reads in reverse direction and /2 reads in forward direction, ie.

                    <-- R/1
 5' =======================> 3' transcript
    F/2 -->

PART 2. Merging assemblies with transabyss-merge

Should you choose to assemble the same dataset with different settings (different k-mer sizes), you can merge the assemblies together into one FASTA file for downstream analyses (with transsabyss-analyze). When a sequence is contained in a longer sequence, the longer sequence is kept.

[2.1] Usage
transabyss-merge --help
[2.2] Running transabyss-merge

Example:

transabyss-merge a.fa b.fa --mink 32 --maxk 64
[2.3] Minimum and maximum k-mer sizes

--mink and --maxk are used to specific the smallest and largest k-mer sizes in the input assemblies.

[2.4] Output merged assembly path

default: ./transabyss-merged.fa

Use option --out to specify the output path.

[2.5] Output sequence prefixes

Use option --prefixes to specify the prefixes of output sequences.

Example:

transabyss-merge a.fa b.fa c.fa --mink 32 --maxk 64 --prefix k32. k48. k64.
file prefix
a.fa k32.
b.fa k48.
c.fa k64.

One prefix for sequences from each input assembly FASTA file. This feature helps you keep track of the origin of each seqeunce in the merged assembly.