Program options for hisat2: 

HISAT2 version 2.1.0 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
Usage: 
  hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <sam>]

  <ht2-idx>  Index filename prefix (minus trailing .X.ht2).
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <SRA accession number>        Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers
  --sra-acc          SRA accession ID

 Alignment:
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)

 Spliced Alignment:
  --pen-cansplice <int>              penalty for a canonical splice site (0)
  --pen-noncansplice <int>           penalty for a non-canonical splice site (12)
  --pen-canintronlen <func>          penalty for long introns (G,-8,1) with canonical splice sites
  --pen-noncanintronlen <func>       penalty for long introns (G,-8,1) with noncanonical splice sites
  --min-intronlen <int>              minimum intron length (20)
  --max-intronlen <int>              maximum intron length (500000)
  --known-splicesite-infile <path>   provide a list of known splice sites
  --novel-splicesite-outfile <path>  report a list of splice sites
  --novel-splicesite-infile <path>   provide a list of novel splice sites
  --no-temp-splicesite               disable the use of splice sites found
  --no-spliced-alignment             disable spliced alignment
  --rna-strandness <string>          specify strand-specific information (unstranded)
  --tmo                              reports only those alignments within known transcriptome
  --dta                              reports alignments tailored for transcript assemblers
  --dta-cufflinks                    reports alignments tailored specifically for cufflinks
  --avoid-pseudogene                 tries to avoid aligning reads to pseudogenes (experimental option)
  --no-templatelen-adjustment        disables template length adjustment for RNA-seq reads

 Scoring:
  --mp <int>,<int>   max and min penalties for mismatch; lower qual = lower penalty <6,2>
  --sp <int>,<int>   max and min penalties for soft-clipping; lower qual = lower penalty <2,1>
  --no-softclip      no soft-clipping
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (L,0.0,-0.2)

 Reporting:
  -k <int> (default: 5) report up to <int> alns per read

 Paired-end:
  -I/--minins <int>  minimum fragment length (0), only valid with --no-spliced-alignment
  -X/--maxins <int>  maximum fragment length (500), only valid with --no-spliced-alignment
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>           write unpaired reads that didn't align to <path>
  --al <path>           write unpaired reads that aligned at least once to <path>
  --un-conc <path>      write pairs that didn't align concordantly to <path>
  --al-conc <path>      write pairs that aligned concordantly at least once to <path>
  (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
  --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --summary-file     print alignment summary to this file.
  --new-summary      print alignment summary in a new style, which is more machine-friendly.
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-head          supppress header lines, i.e. lines starting with @
  --no-sq            supppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.

 Performance:
  -o/--offrate <int> override offrate of index; must be >= index's offrate
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'hisat2's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes
  --remove-chrname   remove 'chr' from reference names in alignment
  --add-chrname      add 'chr' to reference names in alignment 
  --version          print version information and quit
  -h/--help          print this usage message


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Program options for stringtie: 

StringTie v2.2.1 usage:

stringtie <in.bam ..> [-G <guide_gff>] [-l <prefix>] [-o <out.gtf>] [-p <cpus>]
 [-v] [-a <min_anchor_len>] [-m <min_len>] [-j <min_anchor_cov>] [-f <min_iso>]
 [-c <min_bundle_cov>] [-g <bdist>] [-u] [-L] [-e] [--viral] [-E <err_margin>]
 [--ptf <f_tab>] [-x <seqid,..>] [-A <gene_abund.out>] [-h] {-B|-b <dir_path>}
 [--mix] [--conservative] [--rf] [--fr]
Assemble RNA-Seq alignments into potential transcripts.
Options:
 --version : print just the version at stdout and exit
 --conservative : conservative transcript assembly, same as -t -c 1.5 -f 0.05
 --mix : both short and long read data alignments are provided
        (long read alignments must be the 2nd BAM/CRAM input file)
 --rf : assume stranded library fr-firststrand
 --fr : assume stranded library fr-secondstrand
 -G reference annotation to use for guiding the assembly process (GTF/GFF)
 --ptf : load point-features from a given 4 column feature file <f_tab>
 -o output path/file name for the assembled transcripts GTF (default: stdout)
 -l name prefix for output transcripts (default: STRG)
 -f minimum isoform fraction (default: 0.01)
 -L long reads processing; also enforces -s 1.5 -g 0 (default:false)
 -R if long reads are provided, just clean and collapse the reads but
    do not assemble
 -m minimum assembled transcript length (default: 200)
 -a minimum anchor length for junctions (default: 10)
 -j minimum junction coverage (default: 1)
 -t disable trimming of predicted transcripts based on coverage
    (default: coverage trimming is enabled)
 -c minimum reads per bp coverage to consider for multi-exon transcript
    (default: 1)
 -s minimum reads per bp coverage to consider for single-exon transcript
    (default: 4.75)
 -v verbose (log bundle processing details)
 -g maximum gap allowed between read mappings (default: 50)
 -M fraction of bundle allowed to be covered by multi-hit reads (default:1)
 -p number of threads (CPUs) to use (default: 1)
 -A gene abundance estimation output file
 -E define window around possibly erroneous splice sites from long reads to
    look out for correct splice sites (default: 25)
 -B enable output of Ballgown table files which will be created in the
    same directory as the output GTF (requires -G, -o recommended)
 -b enable output of Ballgown table files but these files will be 
    created under the directory path given as <dir_path>
 -e only estimate the abundance of given reference transcripts (requires -G)
 --viral : only relevant for long reads from viral data where splice sites
    do not follow consensus (default:false)
 -x do not assemble any transcripts on the given reference sequence(s)
 -u no multi-mapping correction (default: correction enabled)
 -h print this usage message and exit
 --ref/--cram-ref reference genome FASTA file for CRAM input

Transcript merge usage mode: 
  stringtie --merge [Options] { gtf_list | strg1.gtf ...}
With this option StringTie will assemble transcripts from multiple
input files generating a unified non-redundant set of isoforms. In this mode
the following options are available:
  -G <guide_gff>   reference annotation to include in the merging (GTF/GFF3)
  -o <out_gtf>     output file name for the merged transcripts GTF
                    (default: stdout)
  -m <min_len>     minimum input transcript length to include in the merge
                    (default: 50)
  -c <min_cov>     minimum input transcript coverage to include in the merge
                    (default: 0)
  -F <min_fpkm>    minimum input transcript FPKM to include in the merge
                    (default: 1.0)
  -T <min_tpm>     minimum input transcript TPM to include in the merge
                    (default: 1.0)
  -f <min_iso>     minimum isoform fraction (default: 0.01)
  -g <gap_len>     gap between transcripts to merge together (default: 250)
  -i               keep merged transcripts with retained introns; by default
                   these are not kept unless there is strong evidence for them
  -l <label>       name prefix for output transcripts (default: MSTRG)


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Program options for samtools_sort: 

samtools sort: failed to read header from "-"
sort: invalid option -- 'h'
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
  -o FILE    Write final output to FILE rather than standard output
  -T PREFIX  Write temporary files to PREFIX.nnnn.bam
  --no-PG    do not add a PG line
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --verbosity INT
               Set level of verbosity


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Program options for samtools_view: 

[main_samview] fail to read the header from "-".
[main_samview] fail to read the header from "-".


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Program options for samtools_index: 

Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
Options:
  -b       Generate BAI-format index for BAM files [default]
  -c       Generate CSI-format index for BAM files
  -m INT   Set minimum interval size for CSI indices to 2^INT [14]
  -@ INT   Sets the number of threads [none]
index: invalid option -- 'h'
Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
Options:
  -b       Generate BAI-format index for BAM files [default]
  -c       Generate CSI-format index for BAM files
  -m INT   Set minimum interval size for CSI indices to 2^INT [14]
  -@ INT   Sets the number of threads [none]


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Program options for gffcompare: 

gffcompare v0.12.6
-----------------------------
Usage:
gffcompare [-r <reference_mrna.gtf> [-R]] [-T] [-V] [-s <seq_path>]
    [-o <outprefix>] [-p <cprefix>] 
    {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.gtf>]}

 GffCompare provides classification and reference annotation mapping and
 matching statistics for RNA-Seq assemblies (transfrags) or other generic
 GFF/GTF files.
 GffCompare also clusters and tracks transcripts across multiple GFF/GTF
 files (samples), writing matching transcripts (identical intron chains) into
 <outprefix>.tracking, and a GTF file <outprefix>.combined.gtf which 
 contains a nonredundant set of transcripts across all input files (with
 a single representative transfrag chosen for each clique of matching transfrags
 across samples).

 Options:
 -v display gffcompare version (also --version)
 -i provide a text file with a list of (query) GTF files to process instead
    of expecting them as command line arguments (useful when a large number
    of GTF files should be processed)

 -r reference annotation file (GTF/GFF)
 -R for -r option, consider only the reference transcripts that
    overlap any of the input transfrags (Sn correction)
 -Q for -r option, consider only the input transcripts that
    overlap any of the reference transcripts (Precision correction);
    (Warning: this will discard all "novel" loci!)
 -M discard (ignore) single-exon transfrags and reference transcripts
 -N discard (ignore) single-exon reference transcripts
 -D discard "duplicate" query transfrags (i.e. same intron chain) within
    a single sample (disable "annotation" mode for a single file); 
    this option is automatically enabled when multiple query files are provided
 -S when -D is enabled (or multiple query files are provided), perform a more 
    strict duplicate checking: only discard matching (same intron chain) query 
    transcripts from the same sample if their boundaries are fully contained 
    within (or same with) matching transcripts
    if --strict-match is also given, exact match of all exons is required
 --no-merge : disable close-exon merging (default: merge exons separated by
   "introns" shorter than 5 bases

 -s path to genome sequences (optional); this can be either a multi-FASTA
    file or a directory containing single-fasta files (one for each contig);
    repeats must be soft-masked (lower case) in order to be able to classify
    transfrags as repeats

 -e when estimating exon level accuracy, this is the maximum range
    variation allowed for the free ends of terminal exons (default 100);
	this terminal exon restriction  applies to transcript level accuracy
	when --strict-match option is given
 --strict-match : transcript matching takes into account the -e range
    for terminal exons; code '=' is only assigned if transcript ends are
    within that range, otherwise code '~' is assigned just for intron chain
    match (or significant overlap in the case of single exon transcripts)

 -d max. distance (range) for grouping transcript start sites (100)
 -V verbose processing mode (also shows GFF parser warnings)
 -T do not generate .tmap and .refmap files for each input file
 --chr-stats: the .stats file will show summary and accuracy data
   per reference contig/chromosome
 -j <output.tab> if -r was given, writes novel junctions in this file
 --debug : enables -V and generates additional files: 
    <outprefix>.Q_discarded.lst, <outprefix>.missed_introns.gff,
    <outprefix>.R_missed.lst

Options for the combined GTF output file:
 -p the name prefix to use for consensus transcripts in the 
    <outprefix>.combined.gtf file (default: 'TCONS')
 -C discard matching and "contained" transfrags in the GTF output
    (i.e. collapse intron-redundant transfrags across all query files)
 -A like -C but does not discard intron-redundant transfrags if they start
    with a different 5' exon (keep alternate TSS)
 -X like -C but also discard contained transfrags if transfrag ends stick out
    within the container's introns
 -K for -C/-A/-X, do NOT discard any redundant transfrag matching a reference



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Program options for samtools_merge: 

merge: option requires an argument -- 'h'
Usage: samtools merge [-nurlf] [-h inh.sam] [-b <bamlist.fofn>] <out.bam> <in1.bam> [<in2.bam> ... <inN.bam>]

Options:
  -n         Input files are sorted by read name
  -t TAG     Input files are sorted by TAG value
  -r         Attach RG tag (inferred from file names)
  -u         Uncompressed BAM output
  -f         Overwrite the output BAM if exist
  -1         Compress level 1
  -l INT     Compression level, from 0 to 9 [-1]
  -R STR     Merge file in the specified region STR [all]
  -h FILE    Copy the header in FILE to <out.bam> [in1.bam]
  -c         Combine @RG headers with colliding IDs [alter IDs to be distinct]
  -p         Combine @PG headers with colliding IDs [alter IDs to be distinct]
  -s VALUE   Override random seed
  -b FILE    List of input BAM filenames, one per line [null]
  -X         Use customized index files
  --no-PG    do not add a PG line
      --input-fmt-option OPT[=VAL]
               Specify a single input file format option in the form
               of OPTION or OPTION=VALUE
  -O, --output-fmt FORMAT[,OPT[=VAL]]...
               Specify output format (SAM, BAM, CRAM)
      --output-fmt-option OPT[=VAL]
               Specify a single output file format option in the form
               of OPTION or OPTION=VALUE
      --reference FILE
               Reference sequence FASTA FILE [null]
  -@, --threads INT
               Number of additional threads to use [0]
      --write-index
               Automatically index the output files [off]
      --verbosity INT
               Set level of verbosity


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