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r696: use numbers for hyperlinks

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commit 0217bf2266d3aadd6cd0b0989e7ed339e81eef2a 1 parent 4e7776a
@lh3 authored
Showing with 18 additions and 17 deletions.
  1. +18 −17 README.md
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35 README.md
@@ -1,9 +1,8 @@
####0. In addition to this FAQ, are there any other documentations?
-The algorithms and evaluations are described in the
-[preprint](http://arxiv.org/abs/1203.6364) available from arXiv. The detailed
-command lines are documented in the [fermi
-manpage](https://github.com/lh3/fermi/blob/master/fermi.1).
+The algorithms and evaluations are described in the [preprint][1] available
+from arXiv. The detailed command lines are documented in the [fermi
+manpage][2].
####1. What is fermi?
@@ -23,25 +22,23 @@ contiguity and accuracy to other mainstream assemblers.
In addition to de novo assembly, fermi ultimately aims to preserve all the
information in the raw reads, in particular heterozygous events. SNP and INDEL
calling can be achieved by aligning the fermi unitigs to the reference genome
-and has been shown to be advantageous over other approaches to some extend (see
-also the [preprint](http://arxiv.org/abs/1203.6364)).
+and has been shown to be advantageous over other approaches in some aspects (see
+also the [preprint][1]).
####3. What is the relationship between fermi and SGA?
-Fermi is substantially influenced by [SGA](https://github.com/jts/sga). It
-follows a similar workflow to SGA, including the idea of contrasting read sets.
-On the other hand, the internal implementation of fermi is distinct from that
-of SGA. Fermi uses a novel data structure and different algorithms for almost
-every step. As to the end results, fermi has a similar performance to SGA in
-the intersection of both feature sets and is arguably easier to use. In all,
-both fermi and SGA are viable options for de novo assembly and contrast variant
-calling.
+Fermi is substantially influenced by [SGA][3]. It follows a similar workflow to
+SGA, including the idea of contrasting read sets. On the other hand, the
+internal implementation of fermi is distinct from that of SGA. Fermi uses a
+novel data structure and different algorithms for almost every step. As to the
+end results, fermi has a similar performance to SGA for feature shared between
+them, and is arguably easier to use. In all, both fermi and SGA are viable
+options for de novo assembly and contrast variant calling.
####4. How to run fermi for de novo assembly?
-The [fermi manpage](https://github.com/lh3/fermi/blob/master/fermi.1) shows an
-example. Briefly, if you have Illumina short-insert paired-end reads `read1.fq.gz`
-and `read2.fq.gz`, you can run:
+The [fermi manpage][2] shows an example. Briefly, if you have Illumina
+short-insert paired-end reads `read1.fq.gz` and `read2.fq.gz`, you can run:
run-fermi.pl -Pe ./fermi -t12 read1.fq.gz read2.fq.gz > fmdef.mak
make -f fmdef.mak -j 12
@@ -57,3 +54,7 @@ correction only, you may:
run-fermi.pl -Pe ./fermi -t12 read1.fq.gz read2.fq.gz > fmdef.mak
make -f fmdef.mak -j 12 fmdef.ec.fq.gz
+
+[1]: http://arxiv.org/abs/1203.6364
+[2]: https://github.com/lh3/fermi/blob/master/fermi.1
+[3]: https://github.com/jts/sga
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