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r694: gramatical changes; one more FAQ

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1 parent a3fefd6 commit fb47e99579a321f022919dac5d2fae7ab914666e @lh3 committed Apr 9, 2012
Showing with 13 additions and 5 deletions.
  1. +13 −5 README.md
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18 README.md
@@ -14,10 +14,10 @@ compressed data structure, as the key data representation.
####2. How is fermi different from other assemblers?
-For small genomes, fermi is not much different other assemblers in terms of
-performance. Nonetheless, for mammalian genomes, fermi is one of the few
+For small genomes, fermi is not much different from other assemblers in terms
+of performance. Nonetheless, for mammalian genomes, fermi is one of the few
choices that can do the job in a relatively small memory footprint. It can
-assemble 35-fold human data in 90GB shared memory. It achieves overall similar
+assemble 35-fold human data in 90GB shared memory with an overall similar
contiguity and accuracy to other mainstream assemblers.
In addition to de novo assembly, fermi ultimately aims to preserve all the
@@ -37,7 +37,7 @@ 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.
-####4. How to run fermi?
+####4. How to run fermi for de novo assembly?
The [fermi manpage](https://github.com/lh3/fermi/blob/master/fermi.1) gives an
example. Briefly, if you have Illumina short-insert paired-end reads `read1.fq.gz`
@@ -46,5 +46,13 @@ 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
-to perform assembly. The manpage explains more details.
+to perform assembly using 12 CPU cores. The manpage explains more details.
+
+####5. How to use fermi to correct sequencing errors?
+
+Error correction is an intermediate step in assembly. To perform error
+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

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