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update readme and help information

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This commit is contained in:
Haoyu Cheng
2020-01-02 08:58:50 +08:00
parent 36b42c2d83
commit 1e46798bfb
2 changed files with 4 additions and 6 deletions
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CommandLines.cpp
+2 -1
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@@ -28,7 +28,8 @@ void Print_H(hifiasm_opt_t* asm_opt)
fprintf(stderr, " -k INT k-mer length [%d] (must be < 64)\n", asm_opt->k_mer_length);
///fprintf(stderr, " -w write all overlaps to disk, can accelerate assembly next time [%d]\n", asm_opt->write_index_to_disk);
///fprintf(stderr, " -l load all overlaps from disk, can avoid overlap calculation [%d]\n", asm_opt->load_index_from_disk);
fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n");
///fprintf(stderr, " -i ignore saved overlaps in *.ovlp*.bin files\n");
fprintf(stderr, " -i ignore saved overlaps in *.ovlp* files\n");
fprintf(stderr, " -z INT length of adapters that should be removed [%d]\n", asm_opt->adapterLen);
fprintf(stderr, " -p INT size of popped bubbles [%lld]\n", asm_opt->pop_bubble_size);
fprintf(stderr, " -x FLOAT max overlap drop ratio [%.2g]\n", asm_opt->max_drop_rate);
README.md
+2 -5
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@@ -33,9 +33,7 @@ outputs consist of:
So far hifiasm is still in early development stage, it will output phased
chromosome-level high-quality assembly in the near future. In addition, hifiasm
also outputs three binary files that save all overlap inforamtion
(hifiasm.asm.gfa.aux.bin, hifiasm.asm.gfa.aux.reverse.bin,
hifiasm.asm.gfa.aux.source.bin in default). With these files, hifiasm can avoid
the time-consuming all-to-all overlap calculation step, and do the assembly
(hifiasm.asm.ovlp, hifiasm.asm.ovlp.source, hifiasm.asm.ovlp.reverse in default). With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly
directly and quickly. This might be helpful when you want to get an optimized
assembly by multiple round of experiments with different parameters.
@@ -70,8 +68,7 @@ all overlaps to disk, which can avoid the time-consuming all-to-all overlap
calculation next time. For hifiasm, once the overlap information has been
obtained during the previous run in advance, it is able to load all overlaps
from disk and then directly do assembly. If you want to ignore the pre-computed
overlap information, please specify `-i` or simply delete `*gfa.aux.bin`,
`*gfa.aux.reverse.bin` and `*gfa.aux.source.bin`.
overlap information, please specify `-i` or simply delete `*.ovlp`, `*.ovlp.source` and `*.ovlp.reverse`.
Please note that some old Hifi reads may consist of short adapters. To improve
the assembly quality, adapters should be removed by `-z` as follow: