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update man

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chhylp123
2020-03-22 18:01:04 -04:00
parent 90e290636a
commit 670bd10093
2 changed files with 54 additions and 4 deletions
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4
CommandLines.cpp
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@@ -44,8 +44,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -h show help information\n");
fprintf(stderr, " Trio-partition:\n");
fprintf(stderr, " -P FILE paternal trio index [NULL]\n");
fprintf(stderr, " -M FILE Maternal trio index [NULL]\n");
fprintf(stderr, " -P FILE paternal trio index generated by \"yak count\" [NULL]\n");
fprintf(stderr, " -M FILE Maternal trio index generated by \"yak count\" [NULL]\n");
fprintf(stderr, " -c INT lower bound of the binned k-mer's frequency [%d]\n", asm_opt->min_cnt);
fprintf(stderr, " -d INT upper bound of the binned k-mer's frequency [%d]\n", asm_opt->mid_cnt);

54
hifiasm.1
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@@ -1,4 +1,4 @@
.TH hifiasm 1 "3 Jan 2020" "hifiasm-0.1.0" "Bioinformatics tools"
.TH hifiasm 1 "3 Jan 2020" "hifiasm-0.3.0" "Bioinformatics tools"
.SH NAME
.PP
@@ -181,6 +181,25 @@ Maternal trio index. This index should be generated by
with the maternal short reads. For details of yak, please see
.I [https://github.com/lh3/yak]
.TP 10
.BI -c \ INT
Lower bound of the binned k-mer's frequency [2]. When doing trio binning,
a k-mer is said to be differentiating if it occurs >=
.I [-d upper_bound]
times in one sample
but occurs <
.I [-c lower_bound]
times in the other sample.
.TP 10
.BI -d \ INT
Upper bound of the binned k-mer's frequency [5]. When doing trio binning,
a k-mer is said to be differentiating if it occurs >=
.I [-d upper_bound]
times in one sample
but occurs <
.I [-c lower_bound]
times in the other sample.
@@ -202,6 +221,22 @@ With
.I [-z 20],
hifiasm will remove 20 bases from both ends of each read.
.SH EXAMPLES FRO TRIO
.TP
.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " mat.yak " " mat.fq.gz
Build maternal trio index from mat.fq.gz.
.TP
.BR ./yak " " count " " \-k31 " " \-b37 " " \-t16 " " \-o " " pat.yak " " pat.fq.gz
Build paternal trio index from pat.fq.gz.
.TP
.BR ./hifiasm " " \-o " " NA12878.asm " " \-t " " 32 " " \-P " " pat.yak " " \-M " " mat.yak " " NA12878_1.fq.gz " " NA12878_2.fq.gz
In this example, hifiasm will do trio assembly with 32 CPU threads. The paternal assembly can be found at [NA12878.asm.p.r_utg.gfa],
and the maternal assembly can be found at [NA12878.asm.m.r_utg.gfa].
.SH OUTPUTS
@@ -216,7 +251,7 @@ During the error correction step, hifiasm outputs the following two files:
2. All-to-all overlaps in paf format [outPrefix.ovlp.paf].
.PP
During the assembly step, hifiasm outputs the following four assembly graphs in GFA format:
During the non-trio assembly step, hifiasm outputs the following four assembly graphs in GFA format:
.IP
@@ -236,6 +271,21 @@ This graph collapses different haplotypes.
4. Alternate assembly contig graph [outPrefix.a_ctg.gfa].
This graph consists of all assemblies that are discarded in primary assembly contig graph.
.PP
If you have trio information, hifiasm outputs the following three assembly graphs in GFA format:
.IP
1. Phased maternal unitig graph [outPrefix.m.r_utg.gfa].
This graph keeps the phased maternal assembly.
2. Phased paternal unitig graph [outPrefix.p.r_utg.gfa].
This graph keeps the phased paternal assembly.
3. Haplotype-resolved raw unitig graph [outPrefix.r_utg.gfa].
This graph keeps all haplotype information.
.PP
For each graph, hifiasm also outputs a simplified version without sequences. These simplified
graphs can be easily visualized.