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https://github.com/chhylp123/hifiasm.git
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improve documentation
This commit is contained in:
Heng Li
+3
-1
@@ -46,12 +46,14 @@ void Print_H(hifiasm_opt_t* asm_opt)
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fprintf(stderr, " -n INT small removed unitig threshold [%d]\n", asm_opt->max_short_tip);
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fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
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fprintf(stderr, " -y FLOAT min overlap drop ratio [%.2g]\n", asm_opt->min_drop_rate);
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fprintf(stderr, " -v show version number\n");
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fprintf(stderr, " --version show version number\n");
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fprintf(stderr, " -h show help information\n");
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fprintf(stderr, " Trio-partition:\n");
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fprintf(stderr, " -1 FILE hap1/paternal k-mer dump generated by \"yak count\" []\n");
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fprintf(stderr, " -2 FILE hap2/maternal k-mer dump generated by \"yak count\" []\n");
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fprintf(stderr, " -3 FILE list of hap1/paternal read names []\n");
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fprintf(stderr, " -4 FILE list of hap2/maternal read names []\n");
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fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
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fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);
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@@ -5,34 +5,56 @@
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hifiasm - haplotype-resolved de novo assembler for PacBio Hifi reads.
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.SH SYNOPSIS
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.PP
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hifiasm
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* Assemble HiFi reads:
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.RS 4
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.B hifiasm
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.RB [ -o
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.IR prefix ]
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.RB [ -t
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.IR numThres ]
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.RB [ -r
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.IR roundCorrection ]
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.RB [ -a
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.IR roundGraphClean ]
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.IR nThreads ]
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.RB [ -z
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.IR endTrimLen ]
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.R [options]
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.I input1.fq
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.RI [ input2.fq
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.R [...]]
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.RE
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* Trio binning assembly with yak dumps:
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.RS 4
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.B yak count
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.B -o
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.I paternal.yak
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.B -b37
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.RB [ -t
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.IR nThreads ]
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.RB [ -k
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.IR kmerLen ]
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.RB [ -z
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.IR adapterLen ]
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.RB [ -m
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.IR maxLargeBubbles ]
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.RB [ -p
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.IR maxSmallBubbles ]
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.RB [ -n
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.IR maxSmallUnitig ]
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.RB [ -x
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.IR maxDropRatio ]
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.RB [ -y
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.IR minDropRatio ]
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.RB [ -i ]
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.RB [ -v ]
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.RB [ -h ]
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.I <in_1.fq> <in_2.fq> <...>
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.I paternal.fq.gz
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.br
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.B yak count
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.B -o
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.I maternal.yak
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.B -b37
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.RB [ -t
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.IR nThreads ]
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.RB [ -k
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.IR kmerLen ]
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.I maternal.fq.gz
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.br
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.B hifiasm
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.RB [ -o
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.IR prefix ]
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.RB [ -t
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.IR nThreads ]
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.R [options]
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.B -1
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.I paternal.yak
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.B -2
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.I maternal.yak
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.I child.hifi.fq.gz
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.RE
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.SH DESCRIPTION
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.PP
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@@ -49,9 +71,8 @@ outputs consist of multiple types of assembly graph in GFA format.
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.TP 10
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.BI -o \ FILE
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Prefix of output files [hifiasm.asm]. The outputs of hifiasm include error corrected
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reads in fasta format, all-to-all overlaps in paf format, and four types of assembly
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graph in GFA format. For detailed description of all assembly graphs, please see the
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Prefix of output files [hifiasm.asm]. For detailed description of all assembly
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graphs, please see the
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.B OUTPUTS
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section of this man-page.
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@@ -59,18 +80,18 @@ section of this man-page.
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.BI -t \ INT
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Number of CPU threads used by hifiasm [1].
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.TP
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.BI -h
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Show help information.
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.TP 10
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.BI -v
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.TP
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.BI --version
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Show version number.
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.TP 10
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.BI -h
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Show help information.
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.SS Error correction options
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.TP 10
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.TP
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.BI -k \ INT
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K-mer length [40]. This option must be less than 64.
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@@ -80,7 +101,7 @@ Rounds of haplotype-aware error corrections [2]. This option affects all outputs
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.SS Assembly options
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.TP 10
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.TP
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.BI -a \ INT
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Rounds of assembly graph cleaning [4]. This option is used with
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.B -x
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@@ -90,8 +111,7 @@ Note that unlike
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.BR -r ,
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this option does not affect error corrected reads and all-to-all overlaps.
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.TP 10
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.TP
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.BI -z \ INT
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Length of adapters that should be removed [0]. This option remove
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.I INT
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@@ -100,8 +120,7 @@ Some old Hifi reads may consist of
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short adapters (e.g., 20bp adapter at one end). For such data, trimming short adapters would
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significantly improve the assembly quality.
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.TP 10
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.TP
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.BI -m \ INT
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Maximal probing distance for bubble popping when generating primary/alternate
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contig graphs [10000000]. Bubbles longer than
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@@ -110,8 +129,7 @@ bases will not be popped. For detailed description of these graphs, please see t
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.B OUTPUTS
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section of this man-page.
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.TP 10
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.TP
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.BI -p \ INT
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Maximal probing distance for bubble popping when generating haplotype-resolved processed unitig graph
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without small bubbles [100000]. Bubbles longer than
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@@ -121,16 +139,13 @@ are not the real haplotype information. For detailed description of this graph,
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.B OUTPUTS
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section of this man-page.
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.TP 10
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.TP
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.BI -n \ INT
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A unitig is considered small if it is composed of less than
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.I INT
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reads [3]. Hifiasm may try to remove small unitigs at various steps.
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.TP 10
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.TP
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.BI -x \ FLOAT, -y \ FLOAT
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Max and min overlap drop ratio [0.8, 0.2]. This option is used with
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.BR -r .
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@@ -153,9 +168,11 @@ rounds of short overlap removal with an increasing threshold between
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and
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.BR -y .
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.TP 10
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.TP
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.BI -i
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Ignore saved overlaps in [*.ovlp*] files.
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Ignore error corrected reads and overlaps saved in
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.IR prefix .*.bin
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files.
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Apart from assembly graphs, hifiasm also outputs three binary files
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that save all overlap information during assembly step.
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With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step,
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@@ -168,19 +185,25 @@ with different parameters.
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.TP 10
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.BI -1 \ FILE
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Paternal/haplotype1 k-mer dump generated by
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K-mer dump generated by
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.B yak count
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from the paternal/haplotype1 reads. For details of yak, please see
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.I [https://github.com/lh3/yak]
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from the paternal/haplotype1 reads []
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.TP 10
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.TP
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.BI -2 \ FILE
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Maternal/haplotype2 k-mer dump generated by
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K-mer dump generated by
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.B yak count
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from the maternal/haplotype2 reads. For details of yak, please see
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.I [https://github.com/lh3/yak]
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from the maternal/haplotype2 reads []
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.TP 10
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.TP
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.BI -3 \ FILE
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List of paternal/haplotype1 read names []
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.TP
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.BI -4 \ FILE
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List of maternal/haplotype2 read names []
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.TP
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.BI -c \ INT
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Lower bound of the binned k-mer's frequency [2]. When doing trio binning,
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a k-mer is said to be differentiating if it occurs >=
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@@ -190,7 +213,7 @@ but occurs <
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.B -c
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times in the other sample.
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.TP 10
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.TP
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.BI -d \ INT
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Upper bound of the binned k-mer's frequency [5]. When doing trio binning,
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a k-mer is said to be differentiating if it occurs >=
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@@ -208,38 +231,6 @@ times in the other sample.
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Write additional files to speed up the debugging of graph cleaning
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.SH EXAMPLES
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.TP
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.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " NA12878_1.fq.gz " " NA12878_2.fq.gz
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In this example, hifiasm will be run with 32 CPU threads. The input read files are [NA12878_1.fq.gz]
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and [NA12878_2.fq.gz],
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while all output files can be found at [NA12878.asm.*].
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.TP
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.BR ./hifiasm " " \-o " " butterfly.asm " " \-t " " 32 " " \-z " " 20 " " butterfly.fq.gz
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In this example, hifiasm will be run with 32 CPU threads. The input read file is [butterfly.fq.gz],
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while all output files can be found at [butterfly.asm.*].
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With
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.I [-z 20],
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hifiasm will remove 20 bases from both ends of each read.
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.SH EXAMPLES FRO TRIO
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.TP
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.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " mat.yak " " mat.fq.gz
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Build maternal trio index from mat.fq.gz.
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.TP
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.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " pat.yak " " pat.fq.gz
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Build paternal trio index from pat.fq.gz.
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.TP
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.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-1 " " pat.yak " " \-2 " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
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In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.hap1.p_ctg.gfa],
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and the maternal assembly can be found at [NA12878.asm.hap2.p_ctg.gfa].
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.SH OUTPUTS
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.PP
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@@ -299,8 +290,10 @@ maternal/haplotype2 assembly.
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.RE
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.PP
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For each graph, hifiasm also outputs a simplified version without sequences. These simplified
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graphs can be easily visualized.
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For each graph, hifiasm also outputs a simplified version without sequences for
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the ease of visualization. Hifiasm keeps corrected reads and overlaps in three
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binary files such as it can regenerate assembly graphs from the binary files
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without redoing error correction.
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.PP
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Note that different species need different assembly graphs. For homozygous genomes,
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