Description of functions in Chorus2 ==================================== Chorus2 -------- Function ********* Chorus2 Software for Oligo FISH probe design Parameters *********** .. code-block:: bash -j JELLYFISH, --jellyfish JELLYFISH The path where Jellyfish software installed -b BWA, --bwa BWA The path where BWA software installed -g GENOME, --genome GENOME Fasta format genome file, should include all sequences from genome -i INPUT, --input INPUT Fasta format input file, can be whole genome, a chromosome or one region from genome -s SAVED, --save SAVED The output folder for saving results -p PRIMER, --primer PRIMER A specific 5' labeled R primer for PCR reaction. For example: CGTGGTCGCGTCTCA. (Default is none) -t THREADS, --threads THREADS Number of threads or CPUs to use. (Default: 1) -l LENGTH, --length LENGTH The probe length. (Default: 45) --homology HOMOLOGY The maximum homology(%) between target sequence and probe, range from 50 to 100. (Default: 75) -d DTM, --dtm DTM The minimum value of dTm (hybrid Tm - hairpin Tm), range from 0 to 37. (Default: 10) --skipdtm SKIPDTM skip calculate dtm, for oligo longer than 50. --step STEP The step length for k-mer searching in a sliding window, step length>=1. (Default: 5) --docker DOCKER Only used in Docker version of Chorus --ploidy PLOIDY The ploidy of the given genome (test version). (Default: 2) Usage ****** .. code-block:: bash $ Chorus2 -i TAIR10_chr_all.fas -g TAIR10_chr_all.fas -t 4 \ -j /opt/software/jellyfish/bin/jellyfish -b /opt/software/bwa/bwa -s sample ChorusNGSfilter ---------------- Function ********* ChorusNGSfilter for counting Oligo FISH probe k-mer score using NGS data Parameters *********** .. code-block:: bash -j JELLYFISH, --jellyfish JELLYFISH The path where Jellyfish software installed -g GENOME, --genome GENOME Fasta format genome file, should include all sequences from genome -i INPUT, --input INPUT Fastq format input files contain reads from whole genome shotgun sequencing, files can be gzipped. Multiple files separate with ",". For example: 1.fq.gz,2.fq.gz -jfile JFILE, --jellyfishfile JFILE prebuild jellyfish index file, conflict with input argument. -z {gz,text}, --gzipped {gz,text} Input fastq file is gzipped(gz) or uncompressed(text). (Default: gz) -t THREADS, --threads THREADS Number of threads or CPUs to use. (Default: 1) -k KMER, --kmer KMER Length of k-mer used for counting k-mers in input fastq files. (Default: 17) -p PROBE, --probe PROBE The bed format probe file generated by Chorus -o OUTPUT, --output OUTPUT Output bed format probe file with k-mer score. (Default: output.bed) Usage ****** .. code-block:: bash $ ChorusNGSfilter -i 1.fq.gz,2.fq.gz -z gz -t 4 -g TAIR10_chr_all.fas \ -j /opt/software/jellyfish/bin/jellyfish -p probe.bed -o output.bed ChorusNGSselect ---------------- Function ********* ChorusNGSselect for Oligo FISH probe selection by NGS k-mer score Parameters *********** .. code-block:: bash -i INPUT, --input INPUT Input bed format probe file generated by ChorusNGSfilter -o OUTPUT, --output OUTPUT Output bed format probe file after k-mer score filter. (Default: filtered_output.bed) -m MINK, --min MINK Minimum k-mer score, score < min value will be dropped. For example: 900. Incompatible with parameter '-q/-p' (Default: 0) -l MAXK, --max MAXK Maximum k-mer score, score > max value will be dropped. For example: 2000. Incompatible with parameter '-q/-p' (Default: 10000000) -q MINQUANTILE, --minquantile MINQUANTILE Filter < min% quantile k-mer score, range from 0 to 1. For example: 0.25 means 25% quantile. Incompatible with parameter '-m/-l'. (Default: 0.1) -p MAXQUANTILE, --maxquantile MAXQUANTILE Filter > max% quantile k-mer score, range from 0 to 1. For example: 0.75 means 75% quantile. Incompatible with parameter '-m/-l'. (Default: 0.9) -bs, --bothstrand Keep both + and - strand probes. (Default is True) -ss, --singlestrand Keep only + strand probes. Incompatible with parameter '-bs/--bothstrand' -d DIS, --distance DIS Minimum distance between two adjacent probes. (Default: 25) Usage ****** .. code-block:: bash $ ChorusNGSselect -i ChorusNGSfilter_output.bed -q 0.1 -p 0.9 -d 25 \ -o filtered_output.bed ChorusHomo ----------- Function ********* ChorusHomo for finding probes which can hybridize to a close related species Parameters *********** .. code-block:: bash -j JELLYFISH, --jellyfish JELLYFISH The path where Jellyfish software installed -b BWA, --bwa BWA The path where BWA software installed -ga SOURCE, --source SOURCE Fasta format genome file (GenomeA) which the probe were generated from, should include all sequences from genome -gb TARGET, --target TARGET Fasta format genome file (GenomeB) which the probe will be aligned to, should include all sequences from genome -i INPUT, --input INPUT BED format input file, contains oligo probes generated from Chorus2 -s SAVED, --save SAVED The output folder for saving results -t THREADS, --threads THREADS Number of threads or CPUs to use. (Default: 1) Usage ****** .. code-block:: bash $ ChorusHomo -i probe.bed -ga source_genome.fasta -gb target_genome.fasta \ -j /opt/software/jellyfish/bin/jellyfish -b /opt/software/bwa/bwa \ -t 4 -s sample ChorusNoRef ------------ Function ********* ChorusNoRef for designing oligo-FISH probe for no reference genome Parameters *********** .. code-block:: bash -j JELLYFISH, --jellyfish JELLYFISH The path where Jellyfish software installed -b BWA, --bwa BWA The path where BWA software installed -c BCFTOOLS, --bcftools BCFTOOLS The path where bcftools software installed -m SAMTOOLS, --samtools SAMTOOLS The path where samtools software installed -g GENOME, --genome GENOME Fasta format genome file, should include all sequences from genome -s SAVED, --save SAVED The output folder for saving results --tmp TMP The temporary fold for processing -p PROBE, --probe PROBE Original probe design by Chorus2 and filtered by ChorusNGSfilter -r1 READS1, --reads1 READS1 read1 of species, example: For one Species only: species_R1.fq; for more than one species: species1_R1.fq,species2_R1.fq -r2 READS2, --reads2 READS2 read1 of species, example: For one Species only: species_R2.fq; for more than one species: species1_R2.fq,species2_R2.fq -n NAMES, --names NAMES species name(s), the order must same as r1, r2 -t THREADS, --threads THREADS Number of threads or CPUs to use. (Default: 1) --minkmer MINKMER Probe min count for illumina reads -l LENGTH, --length LENGTH The probe length. (Default: 45) -d MINDEPTH, --mindepth MINDEPTH Minimum depth covered by illumina sequences. (Default: 3) Usage ****** .. code-block:: bash $ ChorusNoRef -g related_genome.fasta -s results -p probes.bed \ -r1 species1_R1.fq,species2_R1.fq -r2 species1_R2.fq,species2_R2.fq \ -n species1,species2 -t 4 --minkmer 0 -l 45 -d 3 ChorusDraftPrebuild -------------------- Function ********* ChorusDraftPrebuild for combining short sequence to speed up oligo search Parameters *********** .. code-block:: bash -i INPUT, --input INPUT Fasta format input file contains short sequences -o OUTPUT, --output OUTPUT Fasta format output file with combined long sequences for speeding up oligo search. (default: output.fa) Usage ****** .. code-block:: bash $ ChorusDraftPrebuild -i short_sequences.fasta -o long_sequences.fasta ChorusGUI ---------- Function ********* User-friendly GUI version of Chorus2 Snapshot *********** .. image:: _static/ChorusGUI_parameter.png Usage ****** .. code-block:: bash $ ChorusGUI ChorusPBGUI ------------ Function ********* A convenient probe seletion software with GUI Snapshot *********** .. image:: _static/ChorusPBGUI.png Usage ****** .. code-block:: bash $ ChorusPBGUI