SeqAn3 Tools (st_*)

These are simple tools to manipulate sequence data.

Available tools

• st_fastq2fasta
  • converts fastq file to fasta file
• st_dna5todna4
  • converts fasta with dna5 alphabet to dna4 alphabet
• st_index_build
  • build a 2FM-Index/Bidirectional FMIndex
• st_index_search
  • searches for given queries using an 2FM-Index
• st_fasta_cut
  • reduces a fasta file to either a certain number of base pairs or a certain number of chromosomes
• st_fasta_info
  • prints information about a fasta file
• st_fasta_dump
  • dumps a fasta file into a text file with delimiter in between and at the end
• st_binary_rev
  • reverses a binary file byte-wise without loading the complete file into memory
• st_scheme_build
  • constructs a search scheme
• st_scheme_stat
  • prints information about a search scheme
• st_bwt_build
  • constructs a bwt
• st_multistring_filter
  • maps indices that can't handle multistring indices, from a single concatenated string back to multi strings
• st_name_id_mapper
  • maps sequence names to ids, or vice versa
• st_sam_filter
  • filters sam files by number of errors
• st_sam_info
  • some infos about the sam file that no one else reports
• st_local_mapper
  • convert output from programs like 'columba' to sam/bam format

Usage

$ st_fastq2fasta input.fastq > output.fasta
Converts a fastq file into a fasta file

$ st_dna5todna4 input.fasta > output.fasta
Converts a dna5 alphabet to dna4 and replaces every occurrence of 'N' with a random 'A', 'C', 'G' or 'T'.

$ st_index_build -v input.dna5.fasta output.dna5.index
$ st_index_build --dna4 -v input.dna4.fasta output.dna4.index
Creates an 2fm-index from a fasta file

$ st_index_search input.dna5.index queries.dna5.fasta results.txt -k 2
$ st_index_search --dna4 input.dna4.index queries.dna4.fasta results.txt -k 2
Searches the index for reads provided by the queries file with 2 errors. Results are stored in results.txt

$ st_fasta_cut --max_chr 2 input.fasta > output.fasta
$ st_fasta_cut --max_bases 1000000 input.fasta > output.fasta
Reduces the number of bases or chromosons in a fasta file

$ st_fasta_info input.fasta lengths
$ st_fasta_info input.fasta names
Prints lengths or names of all fasta file entries

$ st_fasta_dump input.fasta -d '#' -e '$' > output.txt
Converts fasta file into a text file, where each sequence is separated by '#' and a '$' is attached at the end

$ st_binary_rev input.txt > output.txt
reverses the bytes of input.txt

$ st_scheme_build -g "01*0_opt" -k2 > 01star0_k2.ss
constructs a search scheme with two allowed errors, following the optimized 01*0 principle

$ st_scheme_stat --input 01star0_k2.ss --length 100
prints information about a search scheme: number of parts, searches, min/max errors, feasibility, uniqueness, node count, node count for edit distance.

$ st_bwt_build --input sometext.txt > bwt.txt
constructs the bwt of the given text.

Build instructions

1. clone this repository: git clone https://github.com/SGSSGene/seqan3_tools
2. create and enter build folder: mkdir -p seqan3_tools/build; cd $_
3. run cmake with release options: cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-march=native" ..
4. compile with make
5. (optional) put them in your PATH variable PATH="${PATH}:path/to/seqan3_tools/build/bin"